Structure of PDB 7ykk Chain B Binding Site BS01

Receptor Information
>7ykk Chain B (length=735) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FKLPAEFITRPHPSKDHGKETCTAYIHPNVLSSLEINPGSFCTVGKIGEN
GILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQVQPPYAT
KVTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESID
VVITDASDDSLPDVSQLDLNMDDMYGGLGSTHITFSKETQANRKYNLPEP
LSYAAVGGLDKEIESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTG
KTMLLRVVANTSNAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSI
IFIDEIDSIAPNRANDDSGEVESRVVATLLTLMDGMGAAGKVVVIAATNR
PNSVDPALRRPGRFDQEVEIGIPDVDARFDILTKQFSRMSSDRHVLDSEA
IKYIASKTHGYVGADLTALCRESVMKTIQRGLGTDANIDKFSLKVTLKDV
ESAMVDIRPSAMREIFLEMPKVYWSDIGGQEELKTKMKEMIQLPLEASET
FARLGISAPKGVLLYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYV
GESERAIREIFRKARSAAPSIIFFDEIDALSPDRDGSSTSAANHVLTSLL
NEIDGVEELKGVVIVAATNRPDEIDAALLRPGRLDRHIYVGPPDVNARLE
ILKKCTKKFNTEESGVDLHELADRTEGYSGAEVVLLCQEAGLAAIMEDLD
VAKVELRHFEKAFKGIARGITPEMLSYYEEFALRS
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 B 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)		G289 T290 G291 K292 T293 M294 G454 A455 T458
Binding residue
(residue number reindexed from 1)		G248 T249 G250 K251 T252 M253 G413 A414 T417
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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