Structure of PDB 9b5f Chain A Binding Site BS01

Receptor Information
>9b5f Chain A (length=985) Species: 284812 (Schizosaccharomyces pombe 972h-) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TIDEGLYSRQLYVLGHEAMKQMSQSNVLIIGCKGLGVEIAKNVCLAGVKS
VTLYDPQPTRIEDLSSQYFLTEDDIGVPRAKVTVSKLAELNQYVPVSVVD
ELSTEYLKNFKCVVVTETSLTKQLEINDFTHKNHIAYIAADSRGLFGSIF
CDFGENFICTDTDGNEPLTGMIASITDDGVVTMLEETRHGLENGDFVKFT
EVKGMPGLNDGTPRKVEVKGPYTFSIGSVKDLGSAGYNGVFTQVKVPTKI
SFKSLRESLKDPEYVYPDFGKMMRPPQYHIAFQALSAFADAHEGSLPRPR
NDIDAAEFFEFCKKIASTLQFDVELDEKLIKEISYQARGDLVAMSAFLGG
AVAQEVLKATTSKFYPLKQYFYFDSLESLPSSVTISEETCKPRGCRYDGQ
IAVFGSEFQEKIASLSTFLVGAGAIGCEMLKNWAMMGVATGESGHISVTD
MDSIEKSNLNRQFLFRPRDVGKLKSECASTAVSIMNPSLTGKITSYQERV
GPESEGIFGDEFFEKLSLVTNALDNVEARMYVDRRCVFFEKPLLESGTLG
TKGNTQVVVPHLTESYGSSQDPPEKSFPICTLKNFPNRIEHTIAWARDLF
EGLFKQPIDNVNMYLSSPNFLETSLKTSSNPREVLENIRDYLVTEKPLSF
EECIMWARLQFDKFFNNNIQQLLFNFPKDSVTSTGQPFWSGPKRAPTPLS
FDIHNREHFDFIVAAASLYAFNYGLKSETDPAIYERVLAGYNPPPFAPKS
GIANKDKQELKSIADSLPPPSSLVGFRLTPAEFEKDDDSNHHIDFITAAS
NLRAMNYDITPADRFKTKFVAGKIVPAMCTSTAVVSGLVCLELVKLVDGK
KKIEEYKNGFFNLAIGLFTFSDPIASPKMKVNGKEIDKIWDRYNLPDCTL
QELIDYFQKEEGLEVTMLSSGVSLLYANFQPPKKLAERLPLKISELVEQI
TKKKLEPFRKHLVLEICCDDANGEDVEVPFICIKL
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 chain9b5f Chain A Residue 1103 [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]
PDB9b5f Structural basis for transthiolation intermediates in the ubiquitin pathway
Resolution2.78 Å
Binding residue
(original residue number in PDB)		R22 D463 M464 D465 R474 K487 V513 L536 D537 N538
Binding residue
(residue number reindexed from 1)		R9 D450 M451 D452 R461 K474 V500 L523 D524 N525
Annotation score5
Enzymatic activity
Enzyme Commision number 6.2.1.45: E1 ubiquitin-activating enzyme.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004839 ubiquitin activating enzyme activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006974 DNA damage response
GO:0016567 protein ubiquitination
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:9b5f, PDBe:9b5f, PDBj:9b5f
PDBsum9b5f
PubMed39143218
UniProtO94609|UBA1_SCHPO Ubiquitin-activating enzyme E1 1 (Gene Name=ptr3)

[Back to BioLiP]