Structure of PDB 5d1k Chain A Binding Site BS01

Receptor Information
>5d1k Chain A (length=146) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFF
LTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISK
VLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Ligand information
Ligand IDOXL
InChIInChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)/p-2
InChIKeyMUBZPKHOEPUJKR-UHFFFAOYSA-L
SMILES
SoftwareSMILES
ACDLabs 10.04
CACTVS 3.341		[O-]C(=O)C([O-])=O
OpenEye OEToolkits 1.5.0C(=O)(C(=O)[O-])[O-]
FormulaC2 O4
NameOXALATE ION
ChEMBL
DrugBank
ZINC
PDB chain5d1k Chain A Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5d1k Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		W141 Y145
Binding residue
(residue number reindexed from 1)		W140 Y144
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) C85
Catalytic site (residue number reindexed from 1) C84
Enzyme Commision number 2.3.2.23: E2 ubiquitin-conjugating enzyme.
2.3.2.24: (E3-independent) E2 ubiquitin-conjugating enzyme.
Gene Ontology
Molecular Function
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0019787 ubiquitin-like protein transferase activity
GO:0031625 ubiquitin protein ligase binding
GO:0061630 ubiquitin protein ligase activity
GO:0061631 ubiquitin conjugating enzyme activity
Biological Process
GO:0000209 protein polyubiquitination
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016567 protein ubiquitination
GO:0036211 protein modification process
GO:0051865 protein autoubiquitination
GO:0070936 protein K48-linked ubiquitination
Cellular Component
GO:0000151 ubiquitin ligase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5d1k, PDBe:5d1k, PDBj:5d1k
PDBsum5d1k
PubMed26475854
UniProtP62837|UB2D2_HUMAN Ubiquitin-conjugating enzyme E2 D2 (Gene Name=UBE2D2)

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