Structure of PDB 7k5j Chain D Binding Site BS01

Receptor Information
>7k5j Chain D (length=972) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVK
SMTVFDPEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVL
DSLDDVTQLSQFQVVVATDTVSLEDKVKINEFCHSSGIRFISSETRGLFG
NTFVDLGDEFTVLDPTGEEPRTGMVSDIEPDGTVTMLDDNRHGLEDGNFV
RFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYGEYKKGGIFTEVKVP
RKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHNGELP
RTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIPG
VVAFFGGLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQ
PVNSRYDNQIAVFGLDFQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSG
SDGYIVVTDNDSIEKSNLNRQFLFRPKDVGKNKSEVAAEAVCAMNPDLKG
KINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVDARTYVDRRCVFYRK
PLLESGTLGTKGNTQVIIPRLTESYSSSRCTLRSFPNKIDHTIAWAKSLF
QGYFTDSAENVNMYLTQPNFVEQTLKDVKGVLESISDSLSSKPHNFEDCI
KWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEFDIY
NNDHFHFVVAGASLRAYNYGIKKPNVDEYKSVIDHMIIPEFTPNEIDQLV
SSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNCRAQNYFIETADR
QKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLA
LPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGL
EITMLSYGVSLLYASFFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMI
LEICADDKEGEDVEVPFITIHL
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain7k5j Chain D Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7k5j Crystal structures of an E1-E2-ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification.
Resolution3.42 Å
Binding residue
(original residue number in PDB)		G443 A444 D470 N471 D472 K494 K519 V520 L543 D544 N545
Binding residue
(residue number reindexed from 1)		G432 A433 D459 N460 D461 K483 K508 V509 L532 D533 N534
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R21 R481 D544 C600 T601 R603
Catalytic site (residue number reindexed from 1) R10 R470 D533 C580 T581 R583
Enzyme Commision number 6.2.1.45: E1 ubiquitin-activating enzyme.
Gene Ontology
Molecular Function
GO:0004839 ubiquitin activating enzyme activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008641 ubiquitin-like modifier activating enzyme activity
GO:0016874 ligase activity
Biological Process
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006974 DNA damage response
GO:0016567 protein ubiquitination
GO:0036211 protein modification process
GO:0043412 macromolecule modification
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7k5j, PDBe:7k5j, PDBj:7k5j
PDBsum7k5j
PubMed33888705
UniProtP22515|UBA1_YEAST Ubiquitin-activating enzyme E1 1 (Gene Name=UBA1)

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