Structure of PDB 5dka Chain B Binding Site BS01

Receptor Information
>5dka Chain B (length=96) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TSFDCAVCLEVLHQPVRTRCGHVFCRSCIATSLKNNKWTCPYCRAYLPSE
GVPATDVAKRMKSEYKNCAECDTLVCLSEMRAHIRTCQKYIDKYGP
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain5dka Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dka A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		C37 C40 C57 C60
Binding residue
(residue number reindexed from 1)		C5 C8 C25 C28
Annotation score4
Enzymatic activity
Enzyme Commision number 2.3.2.27: RING-type E3 ubiquitin transferase.
Gene Ontology
Molecular Function
GO:0002039 p53 binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0031624 ubiquitin conjugating enzyme binding
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity
Biological Process
GO:0000209 protein polyubiquitination
GO:0002250 adaptive immune response
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016567 protein ubiquitination
GO:0032480 negative regulation of type I interferon production
GO:0039536 negative regulation of RIG-I signaling pathway
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0034098 VCP-NPL4-UFD1 AAA ATPase complex
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5dka, PDBe:5dka, PDBj:5dka
PDBsum5dka
PubMed27411375
UniProtQ96EQ8|RN125_HUMAN E3 ubiquitin-protein ligase RNF125 (Gene Name=RNF125)

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