Structure of PDB 7ykk Chain D Binding Site BS01

Receptor Information
>7ykk 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]
FKLPAEFITRPHPSKDHGKECTAYIHPNVLSSLEINPGSFCTVGKIGENG
ILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQVQPPYATK
VTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESIDV
VITDASDDSLPDVSQLDLNMDDMYGGLGSTHITFSKETQANRKYNLPEPL
SYAAVGGLDKEIESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTGK
TMLLRVVANTSNAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSII
FIDEIDSIAPNRANDDSGEVESRVVATLLTLMDGMGAAGKVVVIAATNRP
NSVDPALRRPGRFDQEVEIGIPDVDARFDILTKQFSRMSSDRHVLDSEAI
KYIASKTHGYVGADLTALCRESVMKTIQRGLGTDANIDKFSLKVTLKDVE
SAMVDIRPSAMREIFLEMPKVYWSDIGGQEELKTKMKEMIQLPLEASETF
ARLGISAPKGVLLYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYVG
ESERAIREIFRKARSAAPSIIFFDEIDALSPDRDGSSTSAANHVLTSLLN
EIDGVEELKGVVIVAATNRPDEIDAALLRPGRLDRHIYVGPPDVNARLEI
LKKCTKKFNTEESGVDLHELADRTEGYSGAEVVLLCQEAGLAAIMEDLDV
AKVELRHFEKAFKGIARGITPEMLSYYEEFALRS
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 chain7ykk 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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PDB7ykk Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition.
Resolution5.9 Å
Binding residue
(original residue number in PDB)		T290 K292 T293 M294 I422 G454 A455 T458
Binding residue
(residue number reindexed from 1)		T248 K250 T251 M252 I380 G412 A413 T416
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
View graph for
Cellular Component
External links
PDB RCSB:7ykk, PDBe:7ykk, PDBj:7ykk
PDBsum7ykk
PubMed36351914
UniProtP32794|AFG2_YEAST ATPase family gene 2 protein (Gene Name=AFG2)

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