Structure of PDB 7ykt Chain B Binding Site BS02

Receptor Information
>7ykt 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 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 chain7ykt Chain B Residue 802 [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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PDB7ykt Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition.
Resolution5.9 Å
Binding residue
(original residue number in PDB)		P559 G560 C561 K563 T564 L565 E617 N660 V725
Binding residue
(residue number reindexed from 1)		P518 G519 C520 K522 T523 L524 E576 N619 V684
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:7ykt, PDBe:7ykt, PDBj:7ykt
PDBsum7ykt
PubMed36351914
UniProtP32794|AFG2_YEAST ATPase family gene 2 protein (Gene Name=AFG2)

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