Structure of PDB 7z11 Chain B Binding Site BS04

Receptor Information
>7z11 Chain B (length=730) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FKLPAEFITRPHPSKDHGKETCTAYIHPNVLSSLEINPGSFCTVGKIGEN
GILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQVQPPYAT
KVTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESID
VVITDASDDNLFYLSPPFIFRKGSTHITFSKETQANRKYNLPEPLSYAAV
GGLDKEIESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTGKTMLLR
VVANTSNAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSIIFIDEI
DSIAPNRANDDSGEVESRVVATLLTLMDGMGAAGKVVVIAATNRPNSVDP
ALRRPGRFDQEVEIGIPDVDARFDILTKQFSRMSSDRHVLDSEAIKYIAS
KTHGYVGADLTALCRESVMKTIQRGLGTDANIDKFSLKVTLKDVESAMVD
IRPSAMREIFLEMPKVYWSDIGGQEELKTKMKEMIQLPLEASETFARLGI
SAPKGVLLYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYVGESERA
IREIFRKARSAAPSIIFFDEIDALSPDRDGSSTSAANHVLTSLLNEIDGV
EELKGVVIVAATNRPDEIDAALLRPGRLDRHIYVGPPDVNARLEILKKCT
KKFNTEESGVDLHELADRTEGYSGAEVVLLCQEAGLAAIMEDLDVAKVEL
RHFEKAFKGIARGITPEMLSYYEEFALRSG
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain7z11 Chain B Residue 902 [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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PDB7z11 Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		I518 G519 P559 G560 C561 S562 K563 T564 L565 N660 I692 G721
Binding residue
(residue number reindexed from 1)		I471 G472 P512 G513 C514 S515 K516 T517 L518 N613 I645 G674
Annotation score4
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7z11, PDBe:7z11, PDBj:7z11
PDBsum7z11
PubMed36097293
UniProtP32794|AFG2_YEAST ATPase family gene 2 protein (Gene Name=AFG2)

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