Structure of PDB 4nnj Chain A Binding Site BS01

Receptor Information
>4nnj Chain A (length=1006) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGV
KSMTVFDPEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNV
LDSLDDVTQLSQFQVVVATDTVSLEDKVKINEFCHSSGIRFISSETRGLF
GNTFVDLGDEFTVLDPTGEEPRTGMVSDIEPDGTVTMLDDNRHGLEDGNF
VRFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYGEYKKGGIFTEVKV
PRKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHNGEL
PRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIP
GVVAFFGGLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTT
QPVNSRYDNQIAVFGLDFQKKIANSKVFLVGSGAIGCEMLKNWALLGLGS
GSDGYIVVTDNDSIEKSNLNRQFLFRPKDVGKNKSEVAAEAVCAMNPDLK
GKINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVDARTYVDRRCVFYR
KPLLESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLCTLRSFPNKID
HTIAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISD
SLSSKPHNFEDCIKWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSG
AKRAPTPLEFDIYNNDHFHFVVAGASLRAYNYGIKSDDSNSKPNVDEYKS
VIDHMIIPEFTPNANLKIQVNDDDPDPDEIDQLVSSLPDPSTLAGFKLEP
VDFEKDDDTNHHIEFITACSNCRAQNYFIETADRQKTKFIAGRIIPAIAT
TTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLALPFFGFSEPIASPKGE
YNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYGVSLLYASF
FPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVP
FITIHL
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 chain4nnj Chain B Residue 101 [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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PDB4nnj Structure of the ubiquitin-activating enzyme loaded with two ubiquitin molecules.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		A444 D470 K494 K519 V520 A542 L543 D544 N545
Binding residue
(residue number reindexed from 1)		A434 D460 K484 K509 V510 A532 L533 D534 N535
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R21 R481 D544 C600 T601 R603 N781 D782
Catalytic site (residue number reindexed from 1) R11 R471 D534 C590 T591 R593 N771 D772
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4nnj, PDBe:4nnj, PDBj:4nnj
PDBsum4nnj
PubMed24816100
UniProtP22515|UBA1_YEAST Ubiquitin-activating enzyme E1 1 (Gene Name=UBA1)

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