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PDB ID Mentions in PubMed Central Article count: 21

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PDB ID Mentions in PubMed Central

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Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

(2005) BMC Struct Biol 5

PubMed: 16105176 | PubMedCentral: PMC1201154 | DOI: 10.1186/1472-6807-5-15

Table 1 The dataset of obligatory and non-obligatory polypeptide chains identified from the PDB LIST OF NON-OBLIGATORY PROTEIN-CHAINS PDB Representative-chain Partner-chain Resolution Names of protein... 1dx5 I M 2.30 Thrombomodulin, Thrombin Heavy Chain 1gua A B 2.00 Rap1A, C-Raf1 1efu A B 2.50 Elongation Factor Tu, Elongation Factor Ts 1avw B A 1.75 Trypsin, Trypsin Inhibitor 1emv A B 1.70 Immunity Protein Im9, Colicin E9 1ay7 B A 1.70 Barstar, Guanyl-Specific Ribonuclease Sa 1stf E I 2.37 Papain (Cys 25 Carboxymethylated), Papain (Cys 25 Carboxymethylated) 3eza B A NMR Histidine-Containing Phosphocarrier Protein H, Phosphotransferase System, Enzyme I 1ggr B A NMR Phosphocarrier Protein Hpr, Pts System, Glucose-Specific Iia Component 1pyt B A 2.35 Procarboxypeptidase A, Procarboxypeptidase A 1pyt B D 2.35 Procarboxypeptidase A, Chymotrypsinogen C 1fle I E 1.90 Elafin, Elastase 1sgp I E 1.40 Turkey Ovomucoid Inhibitor, Streptomyces Griseus Proteinase B 1ycs A B 2.20 P53, P53 1ycs B A 2.20 P53, P53 1efn A B 2.50 Fyn Tyrosine Kinase, Hiv-1 Nef Protein 1efn B A 2.50 HIV-1 Nef Protein, Fyn Tyrosine Kinase 1tx4 A B 1.65 P50-Rho GAP, Transforming protein rhoa 1tx4 B A 1.65 Transforming protein Rhoa, P50-Rho GAP 1a2k C A 2.50 Nuclear Transport Factor 2, Nuclear Transport Factor 2 1fin A B 2.30 Cyclin-Dependent Kinase 2, Cyclin A 1fin B A 2.30 Cyclin A, Cyclin-Dependent Kinase 2 1ak4 A C 2.36 Cyclophilin A, Hiv-1Capsid 1ak4 C A 2.36 Hiv-1Capsid, Cyclophilin A 1dhk A B 1.85 Porcine Pancreatic Alpha-Amylase, Bean Lectin-Like Inhibitor 1gla F G 2.60 Glycerol Kinase, Factor III Glc 1ydr E I 2.20 C-Amp-Dependent Protein Kinase, Protein Kinase Inhibitor Peptide 2pcc A B 2.30 Cytochrome C Peroxidase, Cytochrome C 2pcc B A 2.30 Cytochrome C, Cytochrome C Peroxidase 1d2z A B 2.00 Death Domain Of Pelle, Death Domain Of Tube LIST OF OBLIGATORY PROTEIN-CHAINS PDB Representative chain Partner chain Resolution Names of proteins 1bmq B A 2.50 Interleukin-1 Beta Convertase, Interleukin-1 Beta Convertase 1qdl B A 2.50 Anthranilate Synthase (Trpg-Subunit), Anthranilate Synthase (Trpe-Subunit) 1poi B A 2.50 Glutaconate Coenzyme A-Transferase, Glutaconate Coenzyme A-Transferase 1ihf B A 2.50 Integration Host Factor, Integration Host Factor 1poi B C 2.50 Glutaconate Coenzyme A-Transferase, Glutaconate Coenzyme A-Transferase 1bcr B A 2.50 Serine Carboxypeptidase II, Serine Carboxypeptidase II 1wdc A B 2.00 Scallop Myosin, Scallop Myosin 1wdc A C 2.00 Scallop Myosin, Scallop Myosin 1ryp 1 I 1.90 20S Proteasome, 20S Proteasome 1ryp 1 J 1.90 20S Proteasome, 20S Proteasome 1ryp 1 S 1.90 20S Proteasome, 20S Proteasome 1ryp 1 T 1.90 20S Proteasome, 20S Proteasome 1ryp 1 Z 1.90 20S Proteasome, 20S Proteasome 1ryp 1 2 1.90 20S Proteasome, 20S Proteasome 1kve A B 1.80 Smk Toxin, Smk Toxin 1luc A B 1.50 Bacterial Luciferase, Bacterial Luciferase 1fm0 E D 1.45 Molybdopterin Convertin Factor, Subunit 2, Molybdopterin Convertin Factor, Subunit 1 1fm0 D E 1.45 Molybdopterin Convertin Factor, Subunit 1, Molybdopterin Convertin Factor, Subunit 2 1h2r S L 1.40 Periplasmic [Nife] Hydrogenase Small Subunit, [Nife] Hydrogenase Large Subunit 1h2r L S 1.40 Periplasmic [Nife] Hydrogenase Large Subunit, Periplasmic [Nife] Hydrogenase Small Subunit 1svf C D 1.40 Fusion Glycoprotein, Fusion Glycoprotein 1svf B A 1.40 Fusion Glycoprotein, Fusion Glycoprotein 1hbn B C 1.16 Methyl-Coenzyme M Reductase I Beta Subunit, Methyl-Coenzyme M Reductase I Gamma Subunit 1ycp K J 2.50 Epsilon Thrombin, Epsilon Thrombin 1hfe S L 1.60 Fe-Only Hydrogenase (Smaller Subunit), Fe-Only Hydrogenase (Larger Subunit) 1f95 A B NMR Dynein, Dynein 1a2k A B 2.50 Nuclear Transport Factor 2, Nuclear Transport Factor 2 2thi A B 2.50 Thiaminase I, Thiaminase I 1e5d A B 2.50 Rubredoxin: Oxygen Oxidoreductase, Rubredoxin: Oxygen Oxidoreductase 1b55 B A 2.40 Tyrosine-Protein Kinase Btk, Tyrosine-Protein Kinase Btk 3nos A B 2.40 Endothelial Nitric-Oxide Synthase, Endothelial Nitric-Oxide Synthase 1qfx A B 2.40 pH 2.5 Acid Phosphatase, pH 2.5 Acid Phosphatase 2tmk A B 2.40 Thymidylate Kinase, Thymidylate Kinase 1f37 A B 2.30 Ferredoxin [2Fe-2S], Ferredoxin [2Fe-2S] 1qdn A B 2.30 N-Ethylmaleimide Sensitive Fusion Protein (N), N- Ethylmaleimide Sensitive Fusion Protein (N) 1dcp A B 2.30 Dcoh, Dcoh 1dcp A C 2.30 Dcoh, Dcoh 1dcp A D 2.30 Dcoh, Dcoh 1dcp A E 2.30 Dcoh, Dcoh 1del B A 2.20 Deoxynucleoside Monophosphate Kinase, Deoxynucleoside Monophosphate Kinase 1otg A B 2.10 5-Carboxymethyl-2-Hydroxymuconate Isomerase, 5-Carboxymethyl-2-Hydroxymuconate Isomerase 1bft A B 2.00 Nuclear Factor Nf-Kappa-B P65, Nuclear Factor Nf-Kappa-B P65 1coz A B 2.00 Glycerol-3-Phosphate Cytidylyltransferase, Glycerol-3-Phosphate Cytidylyltransferase 1mka A B 2.00 Beta-Hydroxydecanoyl Thiol Ester Dehydrase, Beta-Hydroxydecanoyl Thiol Ester Dehydrase 1b66 A B 1.90 6-Pyruvoyl Tetrahydropterin Synthase, 6-Pyruvoyl Tetrahydropterin Synthase 1otf A C 1.90 4-Oxalocrotonate Tautomerase, 4-Oxalocrotonate Tautomerase 1otf A D 1.90 4-Oxalocrotonate Tautomerase, 4-Oxalocrotonate Tautomerase 1otf A E 1.90 4-Oxalocrotonate Tautomerase, 4-Oxalocrotonate Tautomerase 1j9l A B 1.90 Stationary Phase Survival Protein, Stationary Phase Survival Protein 1dfn A B 1.90 Defensin HNP-3 – Chain A, Defensin HNP-3 – Chain B 1b93 A B 1.90 Methylglyoxal Synthase, Methylglyoxal Synthase 1b93 A C 1.90 Methylglyoxal Synthase, Methylglyoxal Synthase 1ext B A 1.85 Tumor Necrosis Factor Receptor, Tumor Necrosis Factor Receptor 1kve A C 1.80 Smk Toxin, Smk Toxin 1atl A B 1.80 Atrolysin C, Atrolysin C 1d2v A B 1.75 Myeloperoxidase, Myeloperoxidase 1tvx B A 1.75 Neutrophil Activating Peptide 2 Variant, Neutrophil Activating Peptide 2 Variant 1tvx B C 1.75 Neutrophil Activating Peptide 2 Variant, Neutrophil Activating Peptide 2 Variant 6gsv A B 1.75 Mu Class Glutathione S-Transferase Of Isoenz, Mu Class Glutathione S-Transferase Of Isoenz 1qsg G E 1.75 Enoyl-Reductase, Enoyl-Reductase 1qsg G F 1.75 Enoyl-Reductase, Enoyl-Reductase 1qsg G H 1.75 Enoyl-Reductase, Enoyl-Reductase 1a2z A B 1.73 Pyrrolidone Carboxyl Peptidase, Pyrrolidone Carboxyl Peptidase 1a2z A D 1.73 Pyrrolidone Carboxyl Peptidase, Pyrrolidone Carboxyl Peptidase 1mjh A B 1.70 ATP-Binding Domain Of Protein Mj0577, ATP-Binding Domain Of Protein Mj0577 1dqi A B 1.70 Superoxide Reductase, Superoxide Reductase 1dqi A D 1.70 Superoxide Reductase, Superoxide Reductase 1jqc B A 1.61 Protein R2 Of Ribonucleotide Reductase, Protein R2 Of Ribonucleotide Reductase 1f74 A C 1.60 N-Acetyl-Neuraminate Lyase, N-Acetyl-Neuraminate Lyase 3pvi A B 1.59 Pvuii Endonuclease, Pvuii Endonuclease 1f9z A B 1.50 Glyoxalase I, Glyoxalase I 1jr8 A B 1.50 Erv2 Protein, Mitochondrial, Erv2 Protein, Mitochondrial 1a4i B A 1.50 Methylenetetrahydrofolate Dehydrogenase / Me, Methylenetetrahydrofolate Dehydrogenase / Me 1dvj A B 1.50 Orotidine 5'-Phosphate Decarboxylase, Orotidine 5'-Phosphate Decarboxylase 1qh4 A B 1.41 Creatine Kinase, B Chain, Creatine Kinase, B Chain 2tnf A B 1.40 Tumor Necrosis Factor Alpha, Tumor Necrosis Factor Alpha 3sdh A B 1.40 Hemoglobin I (Homodimer) (Carbon-Monoxy) – C, Hemoglobin I (Homodimer) (Carbon-Monoxy) – C 1i0h A B 1.35 Manganese Superoxide Dismutase Y174F Mutant, Manganese Superoxide Dismutase Y174F Mutant 1dbf A B 1.30 Chorismate Mutase, Chorismate Mutase 1qks A B 1.28 Cytochrome Cd1 Nitrite Reductase, Cytochrome Cd1 Nitrite Reductase 1hbn B E 1.16 Methyl-Coenzyme M Reductase I Beta Subunit, Methyl-Coenzyme M Reductase I Beta Subunit

Publication Year: 2005


Conformational changes in protein loops and helices induced by post-translational phosphorylation.

(2006) PLoS Comput Biol 2

PubMed: 16628247 | PubMedCentral: PMC1440919 | DOI: 10.1371/journal.pcbi.0020032

Accession Numbers The Protein Data Bank ( http://www.rcsb.org/pdb ) accession numbers for the proteins discussed in this paper are as follows: β PGM, (PDB ID: 1LVH); CDK2, phosphorylated (PDB ... D: 1JST); CDK2, unphosphorylated (PDB ID: 1FIN); CDK2/KAP complex (PDB ID: 1FQ1); cyclin A (PDB ID: 1B39); ERK2, phosphorylated (PDB ID: 2ERK); ERK2, unphosphorylated (PDB ID: 1ERK); FixJ, phosphorylated (PDB ID: 1D5W); FixJ, unphosphorylated (PDB ID: 1DCK); GLM, (PDB ID: 1MKI); Hpr, phosphorylated (PDB ID: 1FU0); Hpr, unphosphorylated (PDB ID: 1PTF); LCK, (PDB ID: 3LCK); Pim1, (PDB ID: 2BIK); PMM, (PDB ID: 1K35); Psp, phosphorylated (PDB ID: 1J97); Psp, unphosphorylated (PDB ID: 1L7O); P38 γ, (PDB ID: 1CM8); SpoIIAA, phosphorylated (PDB ID: 1H4X); and SpoIIAA, unphosphorylated (PDB ID: 1H4Z); Spo0A, (PDB ID: 1QMP).

Publication Year: 2006


Protein subunit interfaces: heterodimers versus homodimers.

(2005) Bioinformation 1

PubMed: 17597849 | PubMedCentral: PMC1891636 | DOI: null

References 1 Jones S Thornton JM Proc Natl Acad Sci 1996 93 13 8552589 2 Xu D Protein Engineering 1997 10 999 9464564 3 Tsai CJ Protein Science 1997 6 53 9007976 4 Conte L Lo J Mol Biol 1999 285 2177 ... 925793 5 Chakrabarti P Janin J Proteins 2002 47 334 11948787 6 Brinda KV Protein Eng 2002 15 265 11983927 7 Bahadur RP Proteins 2003 53 708 14579361 8 Nooren IM Thornton JM J Mol Biol 2003 325 991 12527304 9 Caffrey DR Protein Sci 2004 13 190 14691234 10 Zhanhua C Frontiers in Bioscience 2005 10 844 15569623 11 Jones S Thornton JM Prog Biophys Mol Biol 1995 63 31 7746868 12 Lijnzaad P Argos P Proteins 1997 28 333 9223180 13 Dasgupta S Proteins 1997 28 494 9261866 14 Valdar WS Thornton JM J Mol Biol 2001 313 399 11800565 15 Li L Frontiers in Bioscience 2005 10 1977 15769678 16 Lee B Richard EM J Mol Biol 1971 55 379 5551392 17 Rodriguez R Bioinformatics 1998 14 523 9694991 18 Jones S Thornton JM J Mol Biol 1997 272 121 9299342 Figures and Tables Table 1 Dataset Creation Hetero-dimers PDB code Resolution n (Å) Chain one Name of chain one Length Chain two Name of chain two Length 1YCS 2.2 B 53BP2 193 A P53 191 1ABR 2.1 B Abrin-A 267 A Carbohydrate 251 1KU6 2.5 A Acetylcholinesterase 535 B Fasciculin 2 61 1LFD 2.1 B Active ras protein 167 A Ras-interacting domain of ralgds 87 1JIW 1.7 P Alkaline metalloproteinase 470 I Proteinase inhibitor 105 1BPL 2.2 B Alpha-amylase 290 A Alpha-amylase 179 1KXV 1.6 A Alpha-amylase 496 C Camelid VHH domain cab10 119 1TMQ 2.5 A Alpha-amylase 470 B Ragi bifunctional inhibitor 117 1BVN 2.5 P Alpha-amylase 496 T Tendamistat 71 1ACB 2.0 E Alpha-chymotrypsin 241 I Eglin C 63 1CHO 1.8 E Alpha-chymotrypsin 238 I Turkey ovomucoid third domain 53 1CGI 2.3 E Alpha-chymotrypsinogen 245 I Trypsin inhibitor 56 1SLU 1.8 B Anionic trypsin 216 A Ecotin 131 1RE0 2.4 B ARF guanine-nucleotide exchange factor 1 195 A ADP-ribosylation factor 1 162 1KSH 1.8 A ARF-like protein 2 164 B Cyclic phosphodiesterase delta-subunit 141 1MG9 2.3 B ATP dependent CLP protease 143 A Protein YLJA 84 1BRL 2.4 A Bacterial luciferase 340 B Bacterial luciferase 319 1AVA 1.9 A Barley alpha-amylase 2 403 C Barley alpha-amylase/subtilisin inhibitor 181 1B27 2.1 A Barnase 110 D Barstar 90 1LUJ 2.5 A Beta-catenin 501 B Beta-catenin-interacting protein ICAT 71 1S0W 2.3 A Beta-lactamase tem 263 C Beta-lactamase inhibitory protein 165 1BND 2.3 A Brain derived neurotrophic factor 109 B Neurotrophin 3 108 1D4X 1.8 A C. Elegans actin 1/3 368 G Gelsolin 124 1G4Y 1.6 R Calmodulin 147 B Calcium-activated potassium channel RSK2 81 1DTD 1.7 A Carboxypeptidase A2 303 B Metallocarboxypeptidase inhibitor 61 1NW9 2.4 B Catalytic domain of caspase-9 238 A Inhibitor of apoptosis protein 3 91 1OKK 2.1 D Cell division protein 265 A Signal recognition particle protein 290 1H1S 2.0 A Cell division protein kinase 2 296 B Cyclin A2 258 1OHZ 2.2 A Cellulosomal scaffolding protein A 140 B Endo-1 4-beta-xylanase Y 56 1HL6 2.5 A CG8781 protein 119 B Mago nashi protein 137 1P5V 1.7 A Chaperone protein CAF1M 191 B F1 capsule antigen 136 1PDK 2.4 A Chaperone protein PAPD 296 B Protein PAPK 258 1N0L 2.3 A Chaperone protein PAPD 212 B Mature fimbrial protein PAPE 116 1FFG 2.1 B Chemotaxis protein chea 68 A Chemotaxis protein chey 128 1EAY 2 A Chey 128 C Chea 67 1P2M 1.8 A Chymotrypsinogen A 238 B Pancreatic trypsin inhibitor 58 1HCG 2.2 A Coagulation factor 236 B Coagulation factor 51 1V74 2.0 A Colicin D 107 B Colicin D immunity protein 87 1E44 2.4 B Colicin E3 96 A Immunity protein 84 1FR2 1.6 B Colicin E9 131 A Colicin E9 immunity protein 83 1F5Q 2.5 A Cyclin dependent kinase 2 296 B Gamma herpesvirus cyclin 247 1FIN 2.3 A Cyclin-dependent kinase 298 B Cyclin A 260 1BLX 1.9 A Cyclin-dependent kinase 6 305 B P19ink4D 160 1M9E 1.7 A Cyclophilin A 164 D HIV-1 capsid 135 1S6V 1.9 A Cytochrome C peroxidase 294 B Cytochrome C 108 1R8S 1.5 E Cytohesin 2 187 A ADP-ribosylation factor 1 160 1UJZ 2.1 B Designed colicin E7 dnase 127 A Designed colicin E7 immunity protein 87 1NLV 1.8 A Dictyostelium discoideum actin 364 G Gelsolin 123 1H31 1.5 A Diheme cytochrome C 260 B Cytochrome C 138 1EM8 2.1 A DNA polymerase III CHI subunit 147 B DNA polymerase III PSI subunit 110 1JQL 2.5 A DNA polymerase III beta chain 366 B DNA polymerase III delta subunit 140 1EAI 2.4 A Elastase 240 C Chymotrypsin isoinhibitor 1 61 1EFV 2.1 A Electron transfer flavoprotein alpha chain 312 B Electron transfer flavoprotein beta chain 252 1F60 1.7 A Elongation factor EEF1A 440 B Elongation factor EEF1BA 90 1TA3 1.7 B Endo-1 4-beta-xylanase 301 A Xylanase inhibitor protein I 274 1TE1 2.5 B Endo-1 4-xylanase 190 A Xylanase inhibitor protein I 274 3FAP 1.9 A FK506-binding protein 107 B FKBP12-rapamycin associated protein 94 1FCD 2.5 A Flavocytochrome C sulfide dehydrogenase 401 C Flavocytochrome c sulfide dehydrogenase 174 1NF3 2.1 A G25k GTP-binding protein 194 C PAR-6B 123 1NQI 2 B Galactosyltransferase 272 A Alpha lactalbumin 123 1WQ1 2.5 G Gapette 320 R Harvey-RAS 166 1OR0 2.0 B Glutaryl acylase beat subunit 510 A Glutaryl acylase alpha subunit 152 1AXI 2.1 B Growth hormone receptor 191 A Growth hormone 175 2NGR 1.9 B Gtpase activating protein 196 A GTP binding protein 191 1TX4 1.7 A Gtpase-activating protein rhogap 196 B Transforming protein RHOA 174 1AY7 1.7 A Guanyl-specific ribonuclease SA 96 B Barstar 89 1HX1 1.9 A Heat shock cognate 71 KDA 377 B Bag-family molecular chaperone regulator-1 112 1USU 2.2 A Heat shock protein HSP82 246 B AHA1 132 2HBE 2.0 B Hemoglobin 146 A Hemoglobin 141 1GPW 2.4 A Hisf protein 253 B Amidotransferase HISF 200 1CXZ 2.2 A His-tagged transforming protein RHOA 182 B PKN 86 1US7 2.3 B HSP90 chaperone protein kinase 194 A Heat shock protein HSP82 207 1KXP 2.1 D Human vitamin D-binding protein 438 A Actin alpha skeletal muscle 349 1H2A 1.8 L Hydrogenase 534 S Hydrogenase 267 1KA9 2.3 F Imidazole glycerol phosphtate synthase 251 H Imidazole glycerol phosphtate synthase 195 1IBR 2.3 B Importin beta-1 subunit 458 A GTP-binding nuclear protein ran 169 1PVH 2.5 A Interleukin 6 signal transducer 201 B Leukemia inhibitory factor 169 1IAR 2.3 B Interleukin-4 receptor alpha chain 188 A Interleukin 129 1I1R 2.4 A Interleukin-6 receptor beta chain 301 B Viral IL-6 167 1O6S 1.8 A Internalin A 461 B E-cadherin 105 1KI1 2.3 B Intersectin long form 342 A G25k GTP-binding protein 178 2KIN 1.9 A Kinesin 238 B Kinesin 100 1PPF 1.8 E Leukocyte elastase 218 I Ovomucoid inhibitor 56 1OP9 1.9 B Lysozyme C 130 A Hl6 camel VHH fragment 121 1UUZ 1.8 D Lysozyme C 129 A Inhibitor of vertebrate lysozyme 130 1OO0 1.9 A Mago nashi protein 144 B Drosophila Y14 92 1SVX 2.2 B Maltose-binding periplasmic protein 369 A Ankyrin repeat protein OFF7 157 1PQZ 2.1 A MCMV M144 238 B Beta-2-microglobulin 99 1MEE 2.0 A Mesentericopeptidase 275 I Eglin-C 64 1JW9 1.7 B Molybdopterin biosynthesis moeb protein 240 D Molybdopterin converting factor 81 1Q40 2.0 B Mrna export factor MEX67 180 A Mrna transport regulator MTR2 163 1SHW 2.2 B Neural kinase 181 A Ephrin-A5 138 1QAV 1.9 B Neuronal nitric oxide synthase 115 A Alpha-1 syntrophin 90 1E96 2.4 B Neutrophil cytosol factor 2 185 A Ras-related C3 botulinum toxin substrate 1 178 1NPE 2.3 A Nidogen 263 B Laminin gamma-1 chain 164 1GL4 2.0 A Nidogen-1 273 B Proteoglycan core protein 89 1M4U 2.4 A Noggin 199 L Osteogenic protein 1 112 1FYH 2.0 A Nterferon-gamma 242 B Interferon-gamma receptor alpha chain 201 1STF 2.4 E Papain 212 I Stefin B 98 1F34 2.5 A Pepsin A 325 B Major pepsin inhibitor PI-3 138 1UBK 1.2 L Periplasmic hydrogenase large subunit 534 S Periplasmic hydrogenase small subunit 267 1JLT 1.4 B Phospholipase A2 122 A Phospholipase A2 inhibitor 122 1L4Z 2.3 A Plasminogen 248 B Streptokinase 125 1DHK 1.9 A Porcine pancreatic alpha-amylase 495 B Bean lectin-like inhibitor 195 3YGS 2.5 P Procaspase 9 97 C Apoptotic protease activating factor 1 95 1FT1 2.3 B Protein farnesyltransferase 416 A Protein farnesyltransferase 315 1G4U 2.3 S Protein tyrosine phosphatase SPTP 360 R Ras-related C3 botulinum toxin substrate 1 180 1CT4 1.6 E Proteinase 185 I Ovomucoid inhibitor 51 1VG0 2.2 A Rab escort protein 1 481 B Ras-related protein rab-7 182 1F2T 1.6 A Rad50 abc-atpase N-terminal domain 145 B Rad50 abc-atpase C-terminal domain 143 1GUA 2.0 A Rap1A 167 B C-raf1 76 1HE1 2.0 C Ras-related C3 botulinum toxin substrate 1 176 A Exoenzyme S 135 1DS6 2.4 A Ras-related C3 botulinum toxin substrate 2 181 B RHO GDP-dissociation inhibitor 2 179 1C1Y 1.9 A Ras-related protein 167 B Proto-onkogene serine 77 1DFJ 2.5 E Ribonuclease A 124 I Ribonuclease inhibitor 456 1DZB 2.0 A SCFV fragment 1F9 224 X Turkey egg-white lysozyme C 129 1H2S 1.9 A Sensory rhodopsin II 225 B Sensory rhodopsin II transducer 60 1P57 1.8 B Serine protease hepsin heavy chain 247 A Serine protease hepsin light chain 110 4SGB 2.1 E Serine proteinase B 185 I Potato inhibitor 51 1SMP 2.3 A Serratia metallo proteinase 468 I Erwinia chrysanthemi inhibitor 100 1NRJ 1.7 B Signal recognition particle receptor 191 A Docking protein 147 1RJ9 1.9 A Signal recognition protein 277 B Signal recognition particle protein 282 1JTP 1.9 A Single-domain antibody 135 L Lysozyme C 129 1SGD 1.8 E Streptogrisin B 185 I Ovomucoid 51 1LW6 1.5 E Subtilisin BPN 281 I Ubtilisin-chymotrypsin inhibitor-2A 63 2SIC 1.8 E Subtilisin BPN 275 I Streptomyces subtilisin inhibitor 107 1SPB 2.0 S Subtilisin BPN 264 P Subtilisin BPN prosegment 71 1R0R 1.1 E Subtilisin carlsberg 274 I Ovomucoid 51 1CSE 1.2 E Subtilisin carlsberg 274 I Eglin-C 63 1SCJ 2.0 A Subtilisin E 275 B Subtilisin E 71 2SNI 2.1 E Subtilisin novo 275 I Chymotrypsin inhibitor 2 64 1EUC 2.1 B Succinyl-coa synthetase beta chain 393 A Succinyl-coa synthetase alpha chain 306 1ONQ 2.2 A T-cell surface glycoprotein CD1A 274 B Beta-2-microglobulin 99 1JTD 2.3 A Tem-1 beta-lactamase 262 B Beta-lactamase inhibitor protein II 273 1KTZ 2.2 B TGF-beta type II receptor 106 A Transforming growth factor beta 3 82 2TEC 2.0 E Thermitase 279 I Eglin-C 63 1JKG 1.9 B Tip associating protein 180 A NTF2-related export protein 1 139 1D4V 2.2 B TNF-related apoptosis inducing ligand 163 A Death receptor 5 117 1AVW 1.8 A Trypsin 223 B Trypsin inhibitor 171 1BRB 2.1 E Trypsin 223 I BPTI 51 1F5R 1.7 A Trypsin II 216 I Pancreatic trypsin inhibitor 57 1K9O 2.3 E Trypsin II anionic 223 I Alaserpin 376 1D6R 2.3 A Trypsinogen 223 I Bowman-birk proteinase inhibitor 58 1OPH 2.3 B Trypsinogen 223 A Alpha-1 protease inhibitor 375 1P2J 1.4 A Trypsinogen 220 I Pancreatic trypsin inhibitor 56 1S1Q 2.0 A Tumor susceptibility gene 101 protein 137 B Ubiquitin 71 1ITB 2.5 B Type 1 interleukin-1 receptor 310 A Interleukin-1 beta 153 1J7D 1.9 B Ubiquitin-conjugating enzyme E2-17 KDA 149 A MMS2 140 1EUV 1.3 A ULP1 protease 221 B Ubitqutin-like protein SMT3 79 1UGH 1.9 E Uracil-dna glycosylase 223 I Uracil-DNA glycosylase inhibitor 82 1UZX 1.9 A Vacuolar protein sorting-associated protein 135 B Ubiquitin 75 1JTT 2.1 A VH single-domain antibody 133 L Lysozyme 129 1RKE 2.4 A Vinculin 262 B VCL protein 176 1MA9 2.4 A Vitamin D-binding protein 442 B Actin alpha skeletal muscle 356 1YVN 2.1 A Yeast actin 372 G Gelsolin 125 1OXB 2.3 A YDP1P 166 B Osmolarity two-component system protein 124 Homodimers PDB code Resolution(Å) Name of Homodimer Scientific source Chain one Length Chain two Length 1CNZ 1.8 3-isopropylmalate dehydrogenase Salmonella typhimurium A 363 B 363 1AFW 1.8 3-ketoacetyl-coa thiolase Saccharomyces cerevisiae A 390 B 393 1M4I 1.5 Acetyltransferase Escherichia coli A 181 B 176 1LQ9 1.3 Actva-orf6 monooxygenase Streptomyces coelicolor A 112 B 112 1ADE 2 Adenylosucinate synthetase Escherichia coli A 431 B 431 1M7H 2 Adenylylsulfate kinase Penicillium chrysogenum A 203 B 200 1NA8 2.3 ADP-ribosylation binding protein Homo sapiens A 151 B 145 1OR4 2.2 Aerotactic transducer hemat Bacillus subtilis A 169 B 158 1BD0 1.6 Alanine racemase Bacillus stearothermophilus A 381 B 380 1A4U 1.9 Alcohol dehydrogenase Drosophila lebanonensis A 254 B 254 1ALK 2 Alkaline phosphatase Escherichia coli A 449 B 449 1LK9 1.5 Alliin lyase Allium sativum A 425 B 427 1HSS 2.1 Alpha-amylase inhibitor Triticum aestivum A 111 B 111 1S2Q 2.1 Amine oxidase B Homo sapiens A 499 B 494 1EKP 2.5 Amino acid aminotransferase Homo sapiens A 365 B 365 2GSA 2.4 Aminotransferase Synechococcus SP A 427 B 427 1DQT 2 Antigen Mus musculus A 117 B 117 1BJW 1.8 Aspartate aminotransferase Thermus thermophilus A 381 B 381 1JFL 1.9 Aspartate racemase Escherichia coli A 228 B 228 1MJH 1.7 Atp-binding protein Methanococcus jannaschii A 143 B 144 1IRI 2.4 Autocrine motility factor Homo sapiens A 557 B 557 1LR5 1.9 Auxin binding protein Zea mays A 160 B 160 1N80 2.5 Baseplate structural protein Bacteriophage T4 A 328 B 328 1EWZ 2.4 Beta lactamase oxa-10 Pseudomonas aeruginosa A 243 C 243 1EBL 1.8 Beta-ketoacyl-acp Synthase III Escherichia coli A 309 B 309 1N1B 2 Bornyl diphosphate synthase Salvia officinalis A 516 B 519 1KSO 1.7 Calcium-binding protein A3 Homo sapiens A 93 B 93 1JD0 1.5 Carbonic anhydrase Homo sapiens A 260 B 259 1AUO 1.8 Carboxylesterase Pseudomonas fluorescens A 218 B 218 1CDC 2 CD2 Rattus norvegicus A 96 B 96 1F13 2.1 Cellular coagulation factor Homo sapiens A 722 B 719 1NW1 2 Choline kinase Caenorhabditis elegans A 365 B 357 1R5P 2.2 Circadian oscillation regulator Anabaena SP A 90 B 93 1G64 2.1 Cob(I) alamin adenosyltransferase Salmonella typhimurium A 169 B 190 1OTV 2.1 Coenzyme pqq synthesis protein C Klebsiella pneumoniae A 254 B 254 1I0R 1.5 Conserved hypothetical protein Archaeoglobus fulgidus A 161 B 168 1OAC 2 Copper amine oxidase Escherichia coli A 719 B 722 1EAJ 1.4 Coxsackie virus Homo sapiens A 124 B 120 1CHM 1.9 Creatinase Pseudomonas putida A 401 B 401 1S44 1.6 Crustacyanin A1 subunit Homarus gammarus A 180 B 180 1GD7 2 CSAA protein Thermus thermophilus A 109 B 109 1L5B 2 Cyanovirin-N Nostoc ellipsosporum A 101 B 101 1SO2 2.4 Cyclic Phosphodiesterase B Homo sapiens A 363 B 363 1P3W 2.1 Cysteine desulfurase Escherichia coli A 385 B 385 1COZ 2 Cytidylyltransferase Bacillus subtilis A 126 B 126 1P6O 1.1 Cytosine deaminase Saccharomyces cerevisiae A 156 B 161 2DAB 2 D-amino acid aminotransferase Thermophilic bacillus A 280 B 282 1F17 2.3 Dehydrogenase Homo sapiens A 293 B 291 2NAC 1.8 Dehydrogenase Methylotrophic bacterium pseudomonas A 374 B 374 1NFZ 2 Delta-isomerase Escherichia coli A 176 B 180 1D1G 2.1 Dihydrofolate reductase Thermotoga maritima A 164 B 164 1DOR 2 Dihydroorotate dehydrogenase A Lactococcus lactis A 311 B 311 1AD1 2.2 Dihydropteroate synthetase Staphylococcus aureus A 264 B 251 1NU6 2.1 Dipeptidyl peptidase Homo sapiens A 728 B 728 1PE0 1.7 DJ-1 Homo sapiens A 187 B 187 1G1A 2.5 DTDP-D-glucose 4,6-Dehydratase Salmonella enterica A 352 B 352 1BBH 1.8 Electron transport Chromatium vinosum A 131 B 131 1Q8R 1.9 Endodeoxyribonuclease rusa Escherichia coli A 118 B 109 1RVE 2.5 Endonuclease Escherichia coli A 244 B 244 1M9K 2 Endothelial nitric-oxide synthase Homo sapiens A 400 B 401 1P43 1.8 Enolase 1 Saccharomyces cerevisiae A 436 B 436 1JR8 1.5 Erv2 protein mitochondrial Saccharomyces cerevisiae A 105 B 105 1V26 2.5 Fatty-acid-coa synthetase Thermus thermophilus A 489 B 510 1LBQ 2.4 Ferrochelatase Saccharomyces cerevisiae A 356 B 354 1RYA 1.3 Gdp-mannose mannosyl hydrolase Escherichia coli A 160 B 160 1QFH 2.2 Gelation factor Dictyostelium discoideum A 212 B 212 1JV3 2.2 Glcnac1p uridyltransferase Homo sapiens A 490 B 484 1DPG 2 Glucose 6-phosphate dehydrogenase Leuconostoc mesenteroides A 485 B 485 1QXR 1.7 Glucose-6-phosphate isomerase Pyrococcus furiosus A 187 B 187 1EOG 2.1 Glutathione S-transferase Escherichia coli A 208 B 208 1N2A 1.9 Glutathione S-transferase Escherichia coli A 201 B 187 1M0W 1.8 Glutathione synthetase Saccharomyces cerevisiae A 481 B 479 1R9C 1.8 Glutathione transferase Mesorhizobium loti A 125 B 118 1F4Q 1.9 Grancalcin Homo sapiens A 161 B 165 1DQP 1.8 Guanine phosphoribosyltransferase Giardia lamblia A 230 B 230 3SDH 1.4 Hemoglobin Scapharca inaequivalvis A 145 B 145 1IPI 2.2 Holliday junction resolvase Pyrococcus furiosus A 114 B 114 1FWL 2.3 Homoserine kinase Methanococcus jannaschii A 296 B 296 2HHM 2.1 Hydrolase Homo sapiens A 272 B 272 1PP2 2.5 Hydrolase Crotalus atrox R 122 L 122 1FJH 1.7 Hydroxysteroid dehydrogenase Comamonas testosteroni A 236 B 236 1G0S 1.9 Hypothetical Protein Escherichia coli A 201 B 202 1JOG 2.4 Hypothetical protein Haemophilus influenzae A 129 B 129 1PT5 2 Hypothetical protein Escherichia coli A 415 B 415 1QYA 2 Hypothetical Protein Escherichia coli A 293 B 307 1FUX 1.8 Hypothetical protein Escherichia coli A 164 B 163 1J30 1.7 Hypothetical rubrerythrin Sulfolobus tokodaii A 141 B 137 1LHZ 2.3 Immunoglobulin lambda Homo sapiens A 213 B 213 1AA7 2.1 Influenza virus matrix mrotein Influenza virus A 158 B 157 8PRK 1.9 Inorganic pyrophosphatase Saccharomyces cerevisiae A 282 B 282 1R8J 2 Kaia Synechococcus elongatus A 272 B 264 1CQS 1.9 Ketosteroid isomerase Pseudomonas putida A 124 B 124 1AQ6 2 L-2-haloacid dehalogenase Xanthobacter autotrophicus A 245 B 245 1I2W 1.7 Lactamase Bacillus licheniformis A 255 B 256 1BH5 2.2 Lactoylglutathione lyase Homo sapiens A 177 B 182 1QMJ 2.2 Lectin Gallus gallus A 132 B 132 1K75 1.8 L-histidinol dehydrogenase Escherichia coli A 425 B 425 1EHI 2.4 Ligase Leuconostoc mesenteroides A 360 B 347 1NWW 1.2 Limonene-1,2-epoxide hydrolase Rhodococcus erythropolis A 145 B 146 1UC8 2 Lysine biosynthesis enzyme Thermus thermophilus A 240 B 239 1EN5 2.3 Manganese superoxide dismutase Escherichia coli A 205 B 205 1A4I 1.5 Methylenetetrahydrofolate Homo sapiens A 285 B 295 1FC5 2.2 Molybdopterin biosynthesis Escherichia coli A 397 B 396 1JYS 1.9 Mta/sah nucleosidase Escherichia coli A 226 B 226 1LNW 2.1 Multidrug resistance operon repressor Pseudomonas aeruginosa A 137 B 135 1FP3 2 N-acyl-d-glucosamine Sus scrofa A 402 B 402 1FYD 2.3 NAD(+) Synthetase Bacillus subtilis A 271 B 246 1HJ3 1.6 Nitrite reductase Paracoccus pantotrophus A 544 B 542 1G1M 2.3 Nitrogenase iron protein Azotobacter vinelandii A 287 B 289 1G8T 1.1 Nuclease SM2 isoform Seratia marcencsens A 241 B 241 1EYV 1.6 N-utilizing substance protein Mycobacterium tuberculosis A 131 B 133 1M98 2.1 Orange carotenoid protein Arthrospira maxima A 316 B 314 1ORO 2.4 Orotate phosphoribosyltransferase Escherichia coli A 213 B 206 1DVJ 1.5 Orotidine 5'-phosphate decarboxylase Methanobacterium thermoautotrophicum A 239 B 211 1GGQ 2.5 Outer surface protein C Borrelia burgdorferi A 162 B 162 1AOR 2.3 Oxidoreductase Pyrococcus furiosis A 605 B 605 1BMD 1.9 Oxidoreductase Thermus flavus A 327 B 327 1HDY 2.5 Oxidoreductase Homo sapiens A 374 B 374 1N2O 2.1 Pantothenate synthetase Mycobacterium tuberculosis A 279 B 279 1RN5 2.2 Peptide deformylase Leptospira interrogans A 177 B 177 1PN2 2 Peroxisomal hydratase Candida tropicalis A 269 B 267 1PN0 1.7 Phenol 2-monooxygenase Trichosporon cutaneum A 652 C 656 1BXG 2.3 Phenylalanine dehydrogenase Rhodococcus SP A 349 B 347 1M6P 1.8 Phosphate receptor Bos Taurus A 146 B 146 1RQL 2.4 Phosphonoacetaldehyde hydrolase Bacillus cereus A 257 B 257 1O4U 2.5 Phosphoribosyltransferase Thermotoga maritima A 265 B 266 1EZ2 1.9 Phosphotriesterase Pseudomonas diminuta A 328 B 328 1EXQ 1.6 Pol polyprotein Escherichia coli A 147 B 145 1MNA 1.8 Polyketide synthase Streptomyces venezuelae A 276 B 278 1C6X 2.5 Protease Escherichia coli A 99 B 99 1FL1 2.2 Protease Escherichia coli A 192 B 207 1F89 2.4 Protein YLC351C Saccharomyces cerevisiae A 271 B 271 1LHP 2.1 Pyridoxal kinase Ovis aries A 306 B 309 1CBK 2 Pyrophosphokinase Haemophilus influenzae A 160 B 160 1QR2 2.1 Quinone reductase type 2 Homo sapiens A 230 B 230 1EN7 2.4 Recombination endonuclease Bacteriophage T4 A 157 B 157 1EV7 2.4 Restriction endonuclease naei Nocardia aerocolonigenes A 295 B 293 1H8X 2 Ribonuclease Homo sapiens A 125 B 125 1I4S 2.2 Ribonuclease III Aquifex aeolicus A 147 B 147 1KGN 1.9 Ribonucleotide reductase protein Corynebacterium ammoniagenes A 296 B 296 1TLU 1.6 S-adenosylmethionine decarboxylase Thermotoga maritima A 117 B 117 1K6Z 2 Secretion chaperone syce Yersinia pestis A 120 B 119 1K3S 1.9 Sige Salmonella enterica A 106 B 104 1PJQ 2.2 Siroheme synthase Salmonella typhimurium A 447 B 454 1HJR 2.5 Site-specific recombinase Escherichia coli A 158 C 158 3LYN 1.7 Sperm lysine Haliotis fulgens A 122 B 124 2SQC 2 Squalene-hopene Cyclase Alicyclobacillus acidocaldarius A 623 B 623 1SCF 2.2 Stem cell factor Homo sapiens A 116 B 118 1OX8 2.2 Stringent starvation protein B Escherichia coli A 105 B 105 1M3E 2.5 Succinyl-coa Sus scrofa A 459 B 460 1R7A 1.8 Sucrose phosphorylase Bifidobacterium adolescentis A 503 B 503 1SOX 1.9 Sulfite oxidase Gallus gallus A 463 B 458 1L5X 2 Survival protein E Pyrobaculum aerophilum A 270 B 272 1REG 1.9 T4 rega Bacteriophage T4 X 122 Y 120 1MKB 2 Thiol ester dehydrase Escherichia coli A 171 B 171 1QHI 1.9 Thymidine kinase Herpes simplex virus A 304 B 308 1HSJ 2.3 Transcription/sugar binding protein Escherichia coli A 487 B 487 1NY5 2.4 Transcriptional regulator Aquifex aeolicus A 384 B 385 1ON2 1.6 Transcriptional regulator Bacillus subtilis A 135 B 135 1SMT 2.2 Transcriptional repressor Synechococcus A 98 B 101 1TRK 2 Transferase Saccharomyces cerevisiae A 678 B 678 7AAT 1.9 Transferase Gallus gallus A 401 B 401 1KIY 2.4 Trichodiene synthase Fusarium sporotrichioides A 354 B 354 1I8T 2.4 Udp-galactopyranose mutase Escherichia coli A 367 B 367 1F6D 2.5 Udp-n-acetylglucosamine Escherichia coli A 366 B 363 1JP3 1.8 Undecaprenyl pyrophosphate synthase Escherichia coli A 210 B 207 1JMV 1.9 Universal stress protein A Haemophilus influenzae A 140 B 137 1HQO 2.3 URE2 protein Saccharomyces cerevisiae A 221 B 217 9WGA 1.8 Wheat germ agglutinin Triticum vulgaris A 170 B 170 1MI3 1.8 Xylose reductase Candida tenuis A 319 B 319 Figure 1 Difference between heterodimer and homodimer interface properties is shown.

Publication Year: 2005


A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys.

(2007) Proteins 69

PubMed: 17623864 | PubMedCentral: PMC2673351 | DOI: 10.1002/prot.21498

Table I The Number of Top 5 Decoys with rmsd < 10 Å given by EMPIRE and the RosettaDock scoring function Pdb ID a 1CGI 1CHO 2PTC 1TGS 2SNI 2SIC 1CSE 2KAI EMPIRE b 1 5 4 5 5 5 5 5 Roset... aDock c 4 3 2 5 4 5 2 4 Pdb ID 1BRC 1ACB 1BRS 1MAH 1UGH 1DFJ 1FSS 1AVW EMPIRE 5 3 4 5 5 5 3 5 RosettaDock 1 2 4 5 5 4 5 5 Pdb ID 1PPE 1TAB 1UDI 1STF 2TEC 4 HTC 1MLC 1WEJ EMPIRE 5 5 5 5 5 5 2 2 RosettaDock 5 5 5 5 5 5 0 0 Pdb ID 1AHW 1DQJ 1BVK 1FBI 2JEL 1BQL 1JHL 1NQA EMPIRE 0 1 1 5 5 2 1 5 RosettaDock 5 2 5 3 5 5 1 5 Pdb ID 1NMB 1MEL 2VIR 1EO8 1QFU 1IAI 2PCC 1WQ1 EMPIRE 5 5 3 1 4 3 4 4 RosettaDock 5 5 4 1 5 0 3 3 Pdb ID AVZ 1MDA 1IGC 1ATN 1GLA 1SPB 2BTF 1A0Q EMPIRE 0 4 1 5 5 5 3 4 RosettaDock 0 3 2 5 1 5 4 1 Pdb ID 1BTH 1FIN 1FQ1 1GOT 1EFU 3HHR #(≥3) d #(>) EMPIRE 0 0 4 5 2 2 39 21 e RosettaDock 0 0 2 0 0 0 34 10 f a Enzyme/Inhibitor: the first 22 protein complexes (1CGI-4HTC); antibody-antigen: the next 16 protein complexes (1MLC-1IAI); the others: (2PCC to 1A0Q); and the difficult set (1BTH to 3HHR).

Publication Year: 2007


ATP and MO25alpha regulate the conformational state of the STRADalpha pseudokinase and activation of the LKB1 tumour suppressor.

(2009) PLoS Biol 7

PubMed: 19513107 | PubMedCentral: PMC2686265 | DOI: 10.1371/journal.pbio.1000126

(A–C) Resemblance of (A) STRADα/MO25α complex with (B) the CDK2/cyclin A complex (PDB ID 1FIN) and (C) the EGFR/EGFR kinase domain dimer (PDB ID 2GS2).

Publication Year: 2009


Designing coarse grained-and atom based-potentials for protein-protein docking.

(2010) BMC Struct Biol 10

PubMed: 21078143 | PubMedCentral: PMC2996388 | DOI: 10.1186/1472-6807-10-40

Table 2 Dataset 2 contains 40 complexes 1 1A0O 1EFN 1KB5 1TOC 1AGR 1FIN 1MEL 1TX4 1BRS 1FLE 1MKW 1YCS 1BTH 1FSS 1NFD 1YDR 1CBW 1GLA 1NMB 2KAI 1CHO 1GUA 1OSP 2PTC 1CSE 1HWG 1PPF 2TRC 1DHK 1IAI 1STF 3SG... 1DVF 1IGC 1TBQ 4CPA 1EBP 1JHL 1TGS 4HTC 1.

Publication Year: 2010


Allosteric regulation of glycogen synthase kinase 3?: a theoretical study.

(2010) Biochemistry 49

PubMed: 21105670 | PubMedCentral: PMC3005830 | DOI: 10.1021/bi100822q

Table 3 Measures of Activity Level in Kinases kinase other components f PDB code (ref) spine RMSD (Å) c salt bridge (Å) d hydrogen bond (Å) e GSK-3β(p) a   �... 0a0; 2.37 15.44 6.43 GSK-3β(p) a substrate at ABS   1.06 11.59 3.11 GSK-3β(p) a substrate(p) at ABS   1.44 3.37 5.68 GSK-3β(p) a peptide inhibitor at ABS   1.34 13.22 6.56 GSK-3β(p) peptide activator AXIN at an ABS in the C-lobe 1O9U (( 24 )) 0.91 3.89 3.41 GSK-3β(p) peptide inhibitor FRATtide at an ABS in the C-lobe 1GNG (( 51 )) 1.18 3.60 3.14 CDK2 cyclinA at ABS 1FIN (( 33 )) 1.30 3.71 3.24 PDK1 small activator at ABS 3HRF (( 43 )) 1.21 3.46 4.56 aurora-A peptide at ABS 1OL5 (( 42 )) 1.26 3.64 3.28 PKB b peptide at SBS 1O6L (( 41 )) 0.66 3.71 3.22 GSK-3β(p) small drug at SBS 1H8F (( 20 )) 0.96 3.55 3.30 a Outcome of MD simulation.

CDK2 is in surface representation (colored gray), and its residues which are located within 4 Å of the activator protein cyclinA (PDB code 1FIN ) are highlighted in pink( 33 ).

Surprisingly, the location of the new binding site was recently identified as a conserved pocket in the protein kinase family ( 54 ) and was found to be structurally homologous to the PIF pocket of several kinases, where an activator is positioned in the enzyme crystal structures (PDB codes 1FIN , 3HRF , 1OL5 , and 1O6L ).

Publication Year: 2010


Accounting for large amplitude protein deformation during in silico macromolecular docking.

(2011) Int J Mol Sci 12

PubMed: 21541061 | PubMedCentral: PMC3083708 | DOI: 10.3390/ijms12021316

For both cases 1FIN ( Figure 2 ) and 1GOT ( Figure 3 ), when the correct conformation was present in the copy ensemble, the algorithm ranked first solutions close to the native complex structure and c... rrectly selected the bound forms for both the loop and the domain.

Results of an ATTRACT flexible docking simulation of the CDK2-cyclin complex (PDB code 1FIN).

It was found that the method can successfully apply to systems with more than one flexible part (see Figures 2 and 3 ), to systems where the flexible fragment occupies an important fraction of the structure (30% for CDK2-cyclin complex, PDB code 1FIN) or where it can span a large accessible volume ( α - β , γ subunits of transducin, PDB code 1GOT).

Publication Year: 2011


Fascaplysin as a specific inhibitor for CDK4: insights from molecular modelling.

(2012) PLoS One 7

PubMed: 22905154 | PubMedCentral: PMC3419161 | DOI: 10.1371/journal.pone.0042612

The rmsd between the active form ‘hybrid model’ and the experimentally determined CDK4 structure (PDB-ID: 2W9F) is 1.5 Å, this is close to the 1.2 Å found for comparing... the active (PDB-ID: 1FIN) and inactive form (PDB-ID: 2R3I) of CDK2.

Methods Structure preparation, homology modelling and ligand docking The X-ray crystal structure of CDK2 in its active form (PDB-ID: 1FIN [55] ) was used as starting structure for molecular modelling.

In this ‘hybrid’ model the core of the structure is based on the experimentally solved CDK4 structure 2W96, but information from CDK2 (PDB-ID: 1FIN) is used for missing regions and the positioning of the activation loop.

Nine water molecules from the CDK2 X-ray structure (PDB ID: 1FIN) were kept for the MD simulations based on their “conservation” across a set of 21 CDK2 inhibitor structures with a resolution of 1.8 Å or better.

Water molecules were treated using the TIP4P-Ew water model, a re-parameterization of TIP4P [67] with Ewald summation [68] ; five buried crystal waters for CDK2 (PDB-ID 1FIN) and four crystal waters present in equivalent positions in CDK4 were kept in the simulations.

The core of the ‘hybrid model’ for CDK4 was built using the CDK4 structure 2W96 as template, but the modelling strategy also made use of an active form CDK2 structure (PDB-ID: 1FIN) for modelling the T-loop and to impose an active conformation on the C-helix of CDK4.

( A ) Structural overlay of active site residues for CDK2 (green, PDB-ID: 1FIN), CDK4 (blue, PDB-ID: 2W96) and CDK6 (red, PDB-ID: 1G3N).

Publication Year: 2012


A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins.

(2012) PLoS Comput Biol 8

PubMed: 23093928 | PubMedCentral: PMC3475653 | DOI: 10.1371/journal.pcbi.1002738

Lastly, the MPF complex was modeled by superimposing modeled Cdk1 and CycB onto the human Cdk2-Cyclin A complex (1PDB: 1FIN).

Structural analysis of the target proteins Homology modeling of Cdk1, CycB and MPF structures We modeled Cdk1 using human cyclin-dependent kinase 2 (CDK2, PDB code: 1FIN, chain A, sequence identity shared with Cdk1: 64%) as a template.

(A) The alignment of Cdk1 sequence and the template structure PDB: 1FIN.

Publication Year: 2012


On the molecular mechanisms of mitotic kinase activation.

(2012) Open Biol 2

PubMed: 23226601 | PubMedCentral: PMC3513839 | DOI: 10.1098/rsob.120136

( c ) The structure of Cyclin A-bound Cdk2 (PDB code 1FIN) reveals a partly active conformation, with the Lys–Glu salt bridge in place.

Publication Year: 2012


Analysis of substrate specificity and cyclin Y binding of PCTAIRE-1 kinase.

(2012) Cell Signal 24

PubMed: 22796189 | PubMedCentral: PMC3590450 | DOI: 10.1016/j.cellsig.2012.06.018

To test this hypothesis we used the CDK2–cyclin A2 crystal structure (PDB ID: 1FIN ) as a guide to design mutagenesis of interacting residues that would be predicted to disrupt PCTAIRE-1 ... 3;cyclin Y binding.

(A + B) Comparison of the PCTAIRE kinase domain (PDB ID: 3MTL ; Structure Genomics Consortium) with the CDK2 structure bound to cyclin A2 (PDB ID: 1FIN ; [4] ).

(C) Overall structure of CDK2–cyclin A2 complex (PDB ID: 1FIN ).

Publication Year: 2012


A structure-guided approach for protein pocket modeling and affinity prediction.

(2013) J Comput Aided Mol Des 27

PubMed: 24214361 | PubMedCentral: PMC3851759 | DOI: 10.1007/s10822-013-9688-9

PDB codes of the pool of protein structures considered for model guidance in the CDK2 study: 1AQ1, 1FVT, 1FVV, 1GIH, 1B38, 1B39, 1FIN, 1FQ1, 1GY3, 1HCK, 1JST, 1QMZ, 1H08, 1DI8, 1H01, 1H00, 1E9H, 1JVP,... 1KE5, 1KE6, 1KE7, 1KE8, 1KE9, 1H07, 1E1X, 1JSV 26.

Publication Year: 2013


Drug targets for cell cycle dysregulators in leukemogenesis: in silico docking studies.

(2014) PLoS One 9

PubMed: 24454966 | PubMedCentral: PMC3893288 | DOI: 10.1371/journal.pone.0086310

Methods The crystal structures of the 6 proteins-CCNE1 (PDB ID: 1W98), CDK6 (PDB ID: 3NUP), CCND1 (PDB ID: 2W96), CCND3 (PDB ID: 3G33), CDK2 (PDB ID: 1W98) and CCNA1 (PDB ID: 1FIN) were retrieved from... RCSB Protein Data Bank (PDB) ( www.rcsb.org/pdb/home/home.do ).

Publication Year: 2014


Hyperactive Cdc2 kinase interferes with the response to broken replication forks by trapping S.pombe Crb2 in its mitotic T215 phosphorylated state.

(2014) Nucleic Acids Res 42

PubMed: 24861625 | PubMedCentral: PMC4081076 | DOI: 10.1093/nar/gku452

(A) The G146D mutation in the S. pombe Cdc2.1w kinase and the highly conserved Y15 phosphorylation site have been mapped onto the structure of the closely related human CDK2-cyclin A complex (PDB ID: ... FIN) using the program Polyview 3D.

Publication Year: 2014


Break CDK2/Cyclin E1 interface allosterically with small peptides.

(2014) PLoS One 9

PubMed: 25290691 | PubMedCentral: PMC4188581 | DOI: 10.1371/journal.pone.0109154

On the other hand, ten intermediate conformations of CDK2 between inactive (1E1X) and active (1FIN, Chain A) conformations are also generated by the Morph server [45] ( http://molmovdb.mbb.yale.edu/ )...

In the structural modeling and docking selection steps, all the T-loops of the selected CDK2 were built by Rosetta loop modeling algorithm from inactive (1E1X [41] ) and active (1FIN [42] , Chain A) conformations.

Materials and Methods Preparation of the ensemble of CDK2 and initial peptide structures In order to model the flexibility of CDK2, T-loop (residues 150–165) conformations are reconstructed by Rosetta (version 3.1) [44] with KIC algorithm, and ten models are kept for inactive (1E1X [41] ) and active (1FIN [42] , Chain A) conformation, respectively.

Results Peptide selection We constructed the active (PDB ID: 1FIN) and inactive (PDB ID: 1E1X) CDK2 conformations with flexible T-loop (amino acids 150–165) by Rosetta and Morph server totaling 30 models.

Publication Year: 2014


No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions.

(2004) BMC Bioinformatics 5

PubMed: 15096275 | PubMedCentral: PMC419334 | DOI: 10.1186/1471-2105-5-41

c. Ribbon representation of the three-dimensional structure of cdk1 (PDB code 1fin, chain a).

Publication Year: 2004


Cross-talk of phosphorylation and prolyl isomerization of the C-terminal domain of RNA Polymerase II.

(2014) Molecules 19

PubMed: 24473209 | PubMedCentral: PMC4350670 | DOI: 10.3390/molecules19021481

( B ) A magnified view of comparison of activation loops of unphosphorylated (cyan) (PDB ID: 1FIN) [ 90 ] and phosphorylated CDK2 where V163 from inactivated loop moves toward the substrate, blocking ... he proline at P+1.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4378612

> Jeffrey PD , Russo AA , Polyak K , Gibbs E , Hurwitz J , Massague J , Pavletich NP , 1995 , Cyclin A-cyclin-dependent kinase 2 complex , http://www.pdb.org/pdb/explore/explore.do?structureId... 1FIN , Publicly available at RCSB Protein Data Bank.

The complex model of Cln3 and Cdk1 was prepared by Rosetta Docking ( Wang et al., 2007 ), taking the complex structure of Cdk2-cyclin A (PDB ID: 1FIN) as the template.

Publication Year: 2015


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4381582

Notably, focusing the attention on the DFG motif, in contrast with the CDK2 structure bound to cyclin A2 and complexed with the ATP (D in nad F out )(PDBcode: 1FIN), [ 23 , 24 ] the D304 and F305 resi... ues are respectively fixed in the out and in positions confirming the Indirubin-mediated block of PCTAIRE1 in the inactive state conformation ( supplementary figure S2 ).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4463590

( A ) is the interaction network of ATP in monomeric CDK2 (coordinates 1HCK, resolution 1.9 Å); ( B ) is in CDK2/cyclin A dimer (1FIN, 2.3 Å); ( C ) is in the phosphorylated dimer (4EO... , 2.3 Å), respectively; ( D ) The B-factor (Å 2 ) distribution for the ATP atoms across the monomeric CDK2 (in black font) CDK2/cyclin A complex (in green) and phosphorylated dimer (in red).

The yellow, pink and cyan patterns indicate the monomeric CDK2 (free state, coordinates 1HCK), CDK2/cyclin A complex (partially activated form, 1FIN) and phosphorylated dimer (fully activated state, 4EOM), respectively.

Cyclins A and E contain 260 (PDB code 1FIN, residues 173–432) [ 6 ] and 283 amino acids (PDB code 1W98, residues 96–378) [ 91 ], respectively.

Publication Year: 2015