Structure of PDB 9b5l Chain A Binding Site BS01

Receptor Information
>9b5l 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 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 chain9b5l Chain B Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB9b5l Structural basis for transthiolation intermediates in the ubiquitin pathway
Resolution3.3 Å
Binding residue
(original residue number in PDB)		D463 M464 D465 K487 V513 L536 D537 N538
Binding residue
(residue number reindexed from 1)		D450 M451 D452 K474 V500 L523 D524 N525
Annotation score4
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:9b5l, PDBe:9b5l, PDBj:9b5l
PDBsum9b5l
PubMed39143218
UniProtO94609|UBA1_SCHPO Ubiquitin-activating enzyme E1 1 (Gene Name=ptr3)

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