Structure of PDB 7z11 Chain D Binding Site BS02

Receptor Information
>7z11 Chain D (length=734) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KFKLPAEFITRPHPSKDHGKETCTAYIHPNVLSSLEINPGSFCTVGKIGE
NGILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQVQPPYA
TKVTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESI
DVVITDASDDNLFYLSPPFIFRKGSTHITFSKETQANRKYNLPEPLSYAA
VGGLDKEIESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTGKTMLL
RVVANTSNAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSIIFIDE
IDSIAPNRANDDSGEVESRVVATLLTLMDGMGAAGKVVVIAATNRPNSVD
PALRRPGRFDQEVEIGIPDVDARFDILTKQFSRMSSDRHVLDSEAIKYIA
SKTHGYVGADLTALCRESVMKTIQRGLGTDANIDKFSLKVTLKDVESAMV
DIRPSAMREIFLEMPKVYWSDIGGQEELKTKMKEMIQLPLEASETFARLG
ISAPKGVLLYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYVGESER
AIREIFRKARSAAPSIIFFDEIDALSPDRDGSSTSAANHVLTSLLNEIDG
VEELKGVVIVAATNRPDEIDAALLRPGRLDRHIYVGPPDVNARLEILKKC
TKKFNTEESGVDLHELADRTEGYSGAEVVLLCQEAGLAAIMEDLDVAKVE
LRHFEKAFKGIARGITPEMLSYYEEFALRSGSSS
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 C Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7z11 Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		R401 R404
Binding residue
(residue number reindexed from 1)		R355 R358
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)

[Back to BioLiP]