MolNFT v1 · #86169 · protein

RNF8 ring domain structure

4AYC · E3 ubiquitin-protein ligase RNF8: “RNF8 ring domain structure”. X-ray diffraction, 4 ligands (CPQ, ZN, SO4), 2 pockets (best druggability 0.39). MolNFT v1 #86169 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4AYC
Type: protein
Length: 263 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase RNF8
EC: 6.3.2.-
UniProt: O76064
Ligands: CPQ, ZN, SO4, CL
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase RNF8 (EC 6.3.2.-)	protein	136	62% helix, 10% strand	O76064
B	E3 ubiquitin-protein ligase RNF8 (EC 6.3.2.-)	protein	127	58% helix, 11% strand	O76064

Ligands and binding sites

CPQ · N,N-bis(3-D-gluconamidopropyl)deoxycholamide · ligand · chains A
ZN · Zinc ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B
CL · Chloride ion · ion · chains B
GOL · Glycerol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.39	0.80	15	empty
2	52	0.29	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 2032 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

4AYC · RNF8 RING domain structure · the same entry in another collection · chain A against A, TM-score 1.00
O76064 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF8 (O76064) · a predicted model of the same protein · chain A against A, TM-score 0.91

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O76064
Elsewhere: RCSB PDB 4AYC · PDBe 4AYC · UniProt O76064

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