Structure of PDB 8efv Chain A Binding Site BS04

Receptor Information
>8efv Chain A (length=313) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTL
AHVIAHELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSR
QAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAP
LLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTM
RVAKRLFRRVRDFAQVAGEEVITRERALEALAALGLDELGLEKRDREILE
VLILRFGGGPVGLATLATALSEDPGTLEEVHEPYLIRQGLLKRTPRGRVA
TELAYRHLGYPPP
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8efv Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8efv Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor
Resolution2.97 Å
Binding residue
(original residue number in PDB)		R7 P8 Y14 I15 G48 L49 G50 T53 R205
Binding residue
(residue number reindexed from 1)		R3 P4 Y10 I11 G44 L45 G46 T49 R201
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0000400 four-way junction DNA binding
GO:0003677 DNA binding
GO:0005524 ATP binding
GO:0009378 four-way junction helicase activity
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0032508 DNA duplex unwinding
Cellular Component
GO:0005737 cytoplasm
GO:0048476 Holliday junction resolvase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8efv, PDBe:8efv, PDBj:8efv
PDBsum8efv
PubMed
UniProtQ5SL87|RUVB_THET8 Holliday junction branch migration complex subunit RuvB (Gene Name=ruvB)

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