Structure of PDB 5dka Chain B

Receptor sequence

>5dkaB (length=96) Species: 9606 (Homo sapiens)

TSFDCAVCLEVLHQPVRTRCGHVFCRSCIATSLKNNKWTCPYCRAYLPSE
GVPATDVAKRMKSEYKNCAECDTLVCLSEMRAHIRTCQKYIDKYGP

3D structure

• PDB: 5dka A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125.
• Chain: B
• Resolution: 1.55 Å

Enzymatic activity

• Enzyme Commision number: 2.3.2.27: RING-type E3 ubiquitin transferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	B	C37 C40 C57 C60	C5 C8 C25 C28
BS02	ZN	B	C100 C103 H115 C119	C68 C71 H83 C87
BS03	ZN	B	C52 H54 C72 C75	C20 H22 C40 C43
BS04	MG	B	D36 K98	D4 K66

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

External links

• PDB: RCSB:5dka, PDBe:5dka, PDBj:5dka
• PDBsum: 5dka
• PubMed: 27411375
• UniProt: Q96EQ8|RN125_HUMAN E3 ubiquitin-protein ligase RNF125 (Gene Name=RNF125)