Citations in PubMed

Primary Citation PubMed: 10368269 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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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


Mechanistic and functional versatility of radical SAM enzymes.

(2010) F1000 Biol Rep 2

PubMed: 21152342 | PubMedCentral: PMC2996862 | DOI: 10.3410/B2-52

Structure prepared using Pymol Molecular Graphics System [ 74 ] from Protein Data Bank entry 1HFE.

Publication Year: 2010


Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.

(2009) Adv Appl Bioinform Chem 2

PubMed: 21918618 | PubMedCentral: PMC3169947 | DOI: null

Supplementary data Table S1 Heterodimer entries not used to construct the scoring functions PDBID a Chain 1 Chain 2 Residue 1 b Residue 2 c 1b0n A B 111 57 1dce C D 567 331 1dev C D 196 41 1e44 B A 96... 85 1euc B A 396 311 1euv A B 211 86 1f2t A B 149 148 1f34 A B 326 149 1f3u F E 171 118 1f60 A B 458 94 1fs0 G E 230 138 1g8k F E 825 133 1gk9 B A 557 260 1go3 M N 187 107 1gzs A B 180 165 1h0h A B 977 214 1h1r A B 303 258 1h9h * E I 223 36 1hfe M T 421 123 1i2m B A 402 216 1izn A B 286 277 1jdh A B 529 38 1jkg B A 250 140 1jlt A B 122 122 1ka9 F H 252 200 1kfu L S 699 184 1ld8 B A 437 382 1lp1 A B 58 58 1m1e A B 538 81 1mtp A B 323 43 1mu2 A B 555 426 1n1j B A 97 93 1nf3 A C 195 128 1o94 D C 320 264 1o97 D C 320 264 1oo0 A B 147 110 1or7 B F 194 90 1p5v A B 235 147 1q7l A B 198 88 1r8o A B 96 71 1rp3 G H 239 88 1s9d E A 203 164 1tqy G H 424 415 1ubk L S 534 267 1ugp B A 226 203 1vet B A 125 124 1vf6 B D 83 72 6req C D 727 637 Notes: a The entry with * 1h9h, failed in the energy minimization.

Publication Year: 2009


Metabolically engineered bacteria for producing hydrogen via fermentation.

(2008) Microb Biotechnol 1

PubMed: 21261829 | PubMedCentral: PMC3864445 | DOI: 10.1111/j.1751-7915.2007.00009.x

, 1998 ) and D. desulfuricans ATCC 7757 (PDB:1HFE) ( Nicolet et al .

Figure 6 Structure of the [FeFe]‐hydrogenase active centre from Desulfovibrio desulfuricans ATCC 7757 (PDB:1HFE).

Publication Year: 2008


Aerobic damage to [FeFe]-hydrogenases: activation barriers for the chemical attachment of O2.

(2014) Angew Chem Int Ed Engl 53

PubMed: 24615978 | PubMedCentral: PMC4143129 | DOI: 10.1002/anie.201400534

The models for the Dd (PDB id: 3C8Y) and Cp (PDB id: 1HFE) enzymes are almost the same except that Gly 302 and Ala 377 are included only for the Dd protein because they do not form hydrogen bonds in t... e Cp structure.

Publication Year: 2014


In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF.

(2015) Acta Crystallogr D Biol Crystallogr 71

PubMed: 25615856 | PubMedCentral: PMC4304682 | DOI: 10.1107/S139900471401517X

( d ) Iron-only hydrogenase: Fe–S clusters (PDB entry 1hfe ; Nicolet et al. , 2001 ▶ ).

Publication Year: 2015