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PDB ID Mentions in PubMed Central Article count: 5

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PDB ID Mentions in PubMed Central

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Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.

(2005) Nucleic Acids Res 33

PubMed: 15831786 | PubMedCentral: PMC1079965 | DOI: 10.1093/nar/gki349

Table 1 List of protein families and corresponding templates composing set1 Protein name PDB ID Pfam ID UniProt ID Homeobox protein Hox-B1 1B72 Homeobox PBX1_HUMAN Molybdate-dependent transcription re... ulator (Mode) 1B9M HTH_1 MODE_ECOLI Multiple antibiotic resistance protein (Mara) 1BL0 HTH_AraC MARA_ECOLI Transcription factor Mbp1 1BM8 APSES MBP1_YEAST Gere regulatory protein 1FSE GerE GERE_BACSU Hin recombinase 1HCR HTH_7 HIN_SALTY Major centromere autoantigen B 1HLV CENP-B-N CENB_HUMAN Camp receptor protein 1HW5 Crp CRP_ECOLI Trp operon repressor 1JHG Trp_repressor TRPR_ECOLI Lambda repressor/operator complex 1LMB HTH_3 RPC1_LAMBD Purine nucleotide synthesis repressor 1QPZ lacI PURR_ECOLI Transcriptional repressor Smtb 1SMT HTH_5 SMTB_SYNP7 Diphtheria toxin repressor 2DTR Fe_dep_repress DTXR_CORDI Tetracycline repressor 2TCT tetR TER4_ECOLI Table 2 Jackknifed prediction results at different SAM entropy values HMM rep structure fw 0.3 a fw 0.5 a fw 0.7 a fw 0.8 a fw 1.0 a 1B72 0 0 0 0 0 1B9M 0 0 0 0 0 1BL0 0 0 0 1 1 1BM8 0 0 0 0 0 1FSE 2 2 1 1 0 1HCR 2 3 4 4 3 1HLV 2 5 6 6 6 1HW5 0 2 3 3 2 1JHG 0 0 0 0 0 1LMB 2 8 10 8 8 1QPZ 4 5 5 5 4 1SMT 3 3 3 3 3 2DTR 2 3 3 3 3 2TCT 2 7 8 8 7 Total hits 19 38 43 42 37 a fw indicates the entropy value used to derive HMMs from FD multiple alignments.

Publication Year: 2005


Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU.

(2006) BMC Struct Biol 6

PubMed: 17116251 | PubMedCentral: PMC1665450 | DOI: 10.1186/1472-6807-6-24

101 1 × 10 -20 58 Proteins with known 3D structure a PDB code: 1u2w Cadmium efflux system accessory protein CadC Staphylococcus aureus 46.2 2 × 10 -06 34 PDB code: 1r1u Repressor prote... n CzrA b Staphylococcus aureus 45.4 3 × 10 -06 33 PDB code: 1smt Transcriptional repressor SmtB b Synechococcus sp.

Homology modeling and data analysis After careful examination of potential templates the structure of SmtB from Synechococcus PCC7942 (PDB entry: 1smt) [ 31 ], CzrA from Staphylococcus aureus (PDB entry: 1r1u) [ 67 ], and CadC from Staphylococcus aureus pI258 (PDB entry: 1u2w) [ 33 ] were selected for homology modeling.

Fold-recognition servers SPARKS, FUGUE, and 3DPSSM reported SmtB from Synechococcus (PDB entry: 1smt) as the best template with highly significant score.

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


Structural and functional studies of Stf76 from the Sulfolobus islandicus plasmid-virus pSSVx: a novel peculiar member of the winged helix-turn-helix transcription factor family.

(2014) Nucleic Acids Res 42

PubMed: 24682827 | PubMedCentral: PMC4027180 | DOI: 10.1093/nar/gku215

( B ) Superimposed ribbon structures of the winged helix DNA-binding domains of Stf76 (red), SmtB (violet) (PDB ID 1smt chain B), HlyU (blue navy) (PDB ID 3jth chain B), Phr (yellow) (PDB ID 2p4w chai... B) and Ohr (green) (PDB ID 1z9c chain D).

Publication Year: 2014


Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.

(2004) Genome Biol 5

PubMed: 15287974 | PubMedCentral: PMC507877 | DOI: 10.1186/gb-2004-5-8-r52

Hit to PF01442 in domain 2 of htr16 (PF01442 is an apolipoprotein Involved in the uptake of lipids and/or cholesterol) htr17 VNG1733g VNG1734H 536 - 1-91 - - Not applicable htr18 VNG0812g PotD 790 257... 327 - known Lipids PotD is a spermidine/putrescine binding protein Table 2 Annotations for IS element rich regions Name IS-element Method Annotation IS-element rich region 1 VNG5101H/6098H ISH2 Pfam PF01402 CopG ribbon helix, regulates plasmid copy number VNG5102H/6099H - TMHMM Membrane protein, unknown function VNG5104H/6101H - - - VNG5105H/6102H - Meta-Server Hit to 1dhx, Coper binding protein VNG5106H/6103H - TMHMM Membrane protein, unknown function VNG5108H/6105H - Rosetta Hit to 1d1A2, capsid protein/transcription factor VNG5109H/6106H ISH8 Pfam PF01609, transposase DDE domain VNG5112H/6109H - Rosetta Hit to 1dt9A1, translation initiation factor VNG5114H/6111H ISH3 - - VNG5115H/6112H - Pfam PF00589, phage integrase family VNG5116H/6113H - Meta-Server Hit to 1d1qA, phosphotyrosine protein phosphatase VNG5118H/6115H - Rosetta 1he8A3, serine/threonine protein phosphatase VNG5119H/6116H - Meta-Server 1smtA, winged helix (DNA binding) in domain 1 VNG5120H/6117H - Rosetta small protein, 2 hits to 1asu00 phage integrase (weak hits) VNG5122H/6119H ISH7 Pfam PF01609 VNG5123H/6120H ISH7 TMHMM membrane protein, unknown function VNG5124H/6121H - - - IS-element rich region 2 VNG5040H ISH8 Pfam PF01609 VNG5041H/5256H - Rosetta - VNG5042H/5255H Domain 1 ISH9 Rosetta Hit to 1ez3A0, 2 long helices, no function annotation (domain 1) VNG5042H/5255H Domain 2 ISH9 Pfam PF01609 (domain 2) VNG5044H/5253H ISH5 Pfam PF01609 VNG5045H/5252H ISH11 (in ISH5) Pfam PF01609 VNG5047H/5250H - Rosetta Hit to 1am3 (HIV capsid protein), 1.10.1200.30 VNG5048H/5249H - Rosetta Hit to 1ais (cyclin-like fold/TBP fragment), 1.10.472.10 VNG5049H/5248H - Rosetta Hit to 2ezh (transposase/transcription factor), 1.10.10.60 VNG5050H/5247H - Pfam PF03551, PadR repressor tbpB - known tata-box binding protein B Table 3 Predicted transcriptional regulators Protein Cluster number CATH ID Z-score Confidence Other hits Winged helix repressor DNA binding domain VNG0389C 1 1.10.10.10 6.55 0.343 Weak FFAS hit to 1mzbA (ferric uptake gene regulator) 2 1.10.10.10 7.40 0.4 4 1.10.10.10 6.76 0.357 VNG2614H 1 1.10.10.10 6.64 0.313 PSI-BLAST to 1jgsA (winged helix, MarR) 4 1.10.10.60 7.12 0.419 5 1.10.10.10 8.09 0.469 VNG0768H 1 1.10.10.10 7.14 0.385 Not applicable 9 1.10.10.10 8.09 0.481 VNG2369C 1 1.10.10.10 7.14 0.323 Not applicable 5 1.10.10.10 7.69 0.424 VNG2641H 1 1.10.10.10 7.58 0.321 Not applicable VNG1640H 1 1.10.10.10 7.86 0.34 Not applicable VNG5156H 2 1.10.10.10 7.94 0.401 Weak FFAS hit to 1i1gA (LRP-like transcriptional regulator) 3 1.10.10.10 9.36 0.502 4 1.10.10.10 8.55 0.444 VNG5108H 14 1.10.10.10 8.04 0.388 Not applicable VNG6047H 1 1.10.10.10 8.15 0.446 Weak FFAS hit to 1id3D (histone fold) 3 1.10.10.60 8.69 0.524 14 1.10.10.10 10.03 0.58 VNG0703H 1 1.10.10.10 8.17 0.439 PSI-BLAST to 1i1gA (LPR-like regulator) 2 1.10.10.10 7.56 0.37 4 1.10.10.10 7.88 0.428 5 1.10.10.10 7.16 0.369 6 1.10.10.10 8.96 0.505 VNG0462C 1 1.10.10.10 8.42 0.527 PSI-BLAST to 1lnwA (mexR repressor, winged helix fold) PSI-BLAST to ArsR 2 1.10.10.10 9.77 0.621 4 1.10.10.10 7.66 0.489 5 1.10.10.10 8.57 0.545 VNG2014H 14 1.10.10.10 8.72 0.379 Not applicable VNG1229H 1 1.10.10.10 8.80 0.463 Not applicable 4 1.10.10.10 7.95 0.339 VNG0837H 2 1.10.10.10 9.02 0.476 Not applicable 4 1.10.10.10 7.53 0.377 5 1.10.10.10 8.39 0.436 VNG6479H 1 1.10.10.10 9.29 0.53 Not applicable VNG0039H 1 1.10.10.10 9.36 0.478 2 1.10.10.10 8.60 0.438 Weak FFAS hit to 1mkmA (transcriptional regulator IclR, amino-terminal domain) 3 1.10.10.10 9.28 0.438 5 1.10.10.10 9.96 0.522 Homeodomain-like superfamily VNG0293H 3 1.10.10.60 6.14 0.395 PSI-BLAST to 1i1gA (LPR-like regulator) 4 1.10.10.10 7.01 0.427 5 1.10.10.10 6.63 0.393 VNG2074H 11 1.10.10.60 7.09 0.354 Not applicable 1 1.10.10.60 6.03 0.286 VNG6251H 3 1.10.10.60 8.06 0.378 TMHMM predicts 1 TM helix Cyclin A, domain 1 fold VNG2133H 2 1.10.472.10 8.25 0.351 Not applicable VNG6287H 15 1.10.472.10 9.14 0.306 Weak FFAS hit to 1smt-A (SMTB repressor) 4 1.10.472.10 8.93 0.283 2 1.10.472.10 8.50 0.269 VNG0511H 8 1.10.472.10 9.25 0.512 PSI-BLAST hit to 1i1gA VNG1865H 8 1.10.472.10 9.55 0.365 Not applicable 4 1.10.472.10 7.18 0.18

Publication Year: 2004