Structure of PDB 7ykz Chain D Binding Site BS01

Receptor Information
>7ykz Chain D (length=734) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLPAEFITRPHPSKDHGKETCTAYIHPNVLSSLEINPGSFCTVGKIGENG
ILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQVQPPYATK
VTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESIDV
VITDASDDSLPDVSQLDLNMDDMYGGLGSTHITFSKETQANRKYNLPEPL
SYAAVGGLDKEIESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTGK
TMLLRVVANTSNAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSII
FIDEIDSIAPNRANDDSGEVESRVVATLLTLMDGMGAAGKVVVIAATNRP
NSVDPALRRPGRFDQEVEIGIPDVDARFDILTKQFSRMSSDRHVLDSEAI
KYIASKTHGYVGADLTALCRESVMKTIQRGLGTDANIDKFSLKVTLKDVE
SAMVDIRPSAMREIFLEMPKVYWSDIGGQEELKTKMKEMIQLPLEASETF
ARLGISAPKGVLLYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYVG
ESERAIREIFRKARSAAPSIIFFDEIDALSPDRDGSSTSAANHVLTSLLN
EIDGVEELKGVVIVAATNRPDEIDAALLRPGRLDRHIYVGPPDVNARLEI
LKKCTKKFNTEESGVDLHELADRTEGYSGAEVVLLCQEAGLAAIMEDLDV
AKVELRHFEKAFKGIARGITPEMLSYYEEFALRS
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 chain7ykz Chain D Residue 801 [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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PDB7ykz Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition.
Resolution4.3 Å
Binding residue
(original residue number in PDB)		G560 C561 K563 T564 L565 N660 V725
Binding residue
(residue number reindexed from 1)		G518 C519 K521 T522 L523 N618 V683
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
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Biological Process
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Cellular Component
External links
PDB RCSB:7ykz, PDBe:7ykz, PDBj:7ykz
PDBsum7ykz
PubMed36351914
UniProtP32794|AFG2_YEAST ATPase family gene 2 protein (Gene Name=AFG2)

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