MolNFT v1 · #141759 · protein

The ring domain structure of mex-3C

5ZI6 · RNA-binding E3 ubiquitin-protein ligase MEX3C: “The ring domain structure of mex-3C”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.76). MolNFT v1 #141759 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5ZI6
Type: protein
Length: 440 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding E3 ubiquitin-protein ligase MEX3C
EC: 2.3.2.27
UniProt: Q5U5Q3
Ligands: ZN
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	RNA-binding E3 ubiquitin-protein ligase MEX3C (EC 2.3.2.27)	protein	55	16% helix, 27% strand	Q5U5Q3

Ligands and binding sites

ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	997	0.76	0.79	83	empty
2	487	0.61	0.75	51	empty

Interfaces

15 interfaces between chains.

E–F · 549 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 546 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 540 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 539 Å² buried · 8 hydrogen bonds · protein-protein
A–H · 451 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5ZI6 · The RING domain structure of MEX-3C · the same entry in another collection · chain H against H, TM-score 1.00
Q5U5Q3 · AlphaFold monomer V2.0 prediction for RNA-binding E3 ubiquitin- protein ligase MEX3C… · a predicted model of the same protein · chain A against A, TM-score 0.94

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 Q5U5Q3
Elsewhere: RCSB PDB 5ZI6 · PDBe 5ZI6 · UniProt Q5U5Q3

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