Structure of PDB 6o83 Chain A Binding Site BS02

Receptor Information
>6o83 Chain A (length=954) Species: 284812 (Schizosaccharomyces pombe 972h-) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNVLIIGCKGLGVEIAKNVCLAGVKSVTLYDPQPTRIEDLSSQYFLTEDD
IGVPRAKVTVSKLAELNQYVPVSVVDELSTEYLKNFKCVVVTETSLTKQL
EINDFTHKNHIAYIAADSRGLFGSIFCDFGENFICTDTDGNEPLTGMIAS
ITDDGVVTMLEETRHGLENGDFVKFTEVKGMPGLNDGTPRKVEVKGPYTF
SIGSVKDLGSAGYNGVFTQVKVPTKISFKSLRESLKDPEYVYPDFGKMMR
PPQYHIAFQALSAFADAHEGSLPRPRNDIDAAEFFEFCKKIASTLQFDVE
LDEKLIKEISYQARGDLVAMSAFLGGAVAQEVLKATTSKFYPLKQYFYFD
SLESLPSSVTISEETCKPRGCRYDGQIAVFGSEFQEKIASLSTFLVGAGA
IGCEMLKNWAMMGVATGESGHISVTDMDSIEKSNLNRQFLFRPRDVGKLK
SECASTAVSIMNPSLTGKITSYQERVGPESEGIFGDEFFEKLSLVTNALD
NVEARMYVDRRCVFFEKPLLESGTLGTKGNTQVVVPHLTESYGSSQDPPE
KSFPICTLKNFPNRIEHTIAWARDLFEGLFKQPIDNVNMYLSSPNFLETS
LKTSSNPREVLENIRDYLVTEKPLSFEECIMWARLQFDKFFNNNIQQLLF
NFPKDSVTSTGQPFWSGPKRAPTPLSFDIHNREHFDFIVAAASLYAFNYG
LKSETDPAIYERVLAGYNPPPFAPDKQELKSIADSLPPPSSLVGFRLTPA
EFEKDDDSNHHIDFITAASNLRAMNYDITPADRFKTKFVAGKIVPAMCTS
TAVVSGLVCLELVKLVDGKKKIEEYKNGFFNLAIGLFTFSDPIASPKMKV
NGKEIDKIWDRYNLPDCTLQELIDYFQKEEGLEVTMLSSGVSLLYANFQP
PKKLAERLPLKISELVEQITKKKLEPFRKHLVLEICCDDANGEDVEVPFI
CIKL
Ligand information
Ligand IDVMX
InChIInChI=1S/C13H21N7O5S/c14-2-1-3-26(23,24)19-4-7-9(21)10(22)13(25-7)20-6-18-8-11(15)16-5-17-12(8)20/h5-7,9-10,13,19,21-22H,1-4,14H2,(H2,15,16,17)/t7-,9-,10-,13-/m1/s1
InChIKeyGCNSCCULRVBOML-QYVSTXNMSA-N
SMILES
SoftwareSMILES
CACTVS 3.352NCCC[S](=O)(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.352NCCC[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CNS(=O)(=O)CCCN)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CNS(=O)(=O)CCCN)O)O)N
FormulaC13 H21 N7 O5 S
Name5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine
ChEMBL
DrugBank
ZINCZINC000058638696
PDB chain6o83 Chain A Residue 1108 [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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PDB6o83 Structural basis for adenylation and thioester bond formation in the ubiquitin E1.
Resolution3.153 Å
Binding residue
(original residue number in PDB)		I438 D463 M464 D465 K487 V513 A535 D537 N538 T561 C593
Binding residue
(residue number reindexed from 1)		I401 D426 M427 D428 K450 V476 A498 D500 N501 T524 C556
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) R474 D537 C593 T594 K596
Catalytic site (residue number reindexed from 1) R437 D500 C556 T557 K559
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:0008641 ubiquitin-like modifier activating enzyme activity
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
GO:0036211 protein modification process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6o83, PDBe:6o83, PDBj:6o83
PDBsum6o83
PubMed31235585
UniProtO94609|UBA1_SCHPO Ubiquitin-activating enzyme E1 1 (Gene Name=ptr3)

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