Structure of PDB 7wd3 Chain F Binding Site BS05

Receptor Information
>7wd3 Chain F (length=722) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLPAEFITRPHPSKDHGKETCTAYIHPNVLSSLEINPGSFCTVGKIGENG
ILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQVQPPYATK
VTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESIDV
VITDAFYLSPPFIFRKGSTHITFSKETQANRKYNLPEPLSYAAVGGLDKE
IESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTGKTMLLRVVANTS
NAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSIIFIDEIDSIAPN
RANDDSGEVESRVVATLLTLMDGMGAAGKVVVIAATNRPNSVDPALRRPG
RFDQEVEIGIPDVDARFDILTKQFSRMSSDRHVLDSEAIKYIASKTHGYV
GADLTALCRESVMKTIQRGLGTDANIDKFSLKVTLKDVESAMVDIRPSAM
REIFLEPKVYWSDIGGQEELKTKMKEMIQLPLEASETFARLGISAPKGVL
LYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYVGESERAIREIFRK
ARSAAPSIIFFDEIDALSPDRDGSSTSAANHVLTSLLNEIDGVEELKGVV
IVAATNRPDEIDAALLRPGRLDRHIYVGPPDVNARLEILKKCTKKFNTEE
SGVDLHELADRTEGYSGAEVVLLCQEAGLAAIMEDLDVAKVELRHFEKAF
KGIARGITPEMLSYYEEFALRS
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain7wd3 Chain F Residue 805 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7wd3 Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		I518 P559 G560 C561 S562 L565 N660 I692 G721 A722
Binding residue
(residue number reindexed from 1)		I464 P505 G506 C507 S508 L511 N606 I638 G667 A668
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.10: non-chaperonin molecular chaperone ATPase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0009410 response to xenobiotic stimulus
GO:0034214 protein hexamerization
GO:0042254 ribosome biogenesis
GO:0042273 ribosomal large subunit biogenesis
Cellular Component
GO:0005737 cytoplasm
GO:0030687 preribosome, large subunit precursor

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7wd3, PDBe:7wd3, PDBj:7wd3
PDBsum7wd3
PubMed36351914
UniProtP32794|AFG2_YEAST ATPase family gene 2 protein (Gene Name=AFG2)

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