Structure of PDB 6nya Chain D Binding Site BS01

Receptor Information
>6nya Chain D (length=987) 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
AKRAPTPLEFDIYNNDHFHFVVAGASLRAYNYGIKSDSKPNVDEYKSVID
HMIIPEFTPNIDQLVSSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITAC
SNCRAQNYFIETADRQKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDN
KTDIEQYKNGFVNLALPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKGDI
KLSDLIEHFEKDEGLEITMLSYGVSLLYASFFPPKKLKERLNLPITQLVK
LVTKKDIPAHVSTMILEICADDKEGEDVEVPFITIHL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain6nya Chain D Residue 1202 [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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PDB6nya Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34.
Resolution2.065 Å
Binding residue
(original residue number in PDB)		R21 A444 D470 D472 N478 R481 Q482 K494 K519 V520 L543 D544 N545
Binding residue
(residue number reindexed from 1)		R11 A434 D460 D462 N468 R471 Q472 K484 K509 V510 L533 D534 N535
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R21 R481 D544 C600 T601 R603
Catalytic site (residue number reindexed from 1) R11 R471 D534 C590 T591 R593
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:6nya, PDBe:6nya, PDBj:6nya
PDBsum6nya
PubMed31341161
UniProtP22515|UBA1_YEAST Ubiquitin-activating enzyme E1 1 (Gene Name=UBA1)

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