MolNFT v1 · #101414 · protein

Structure of coiled-coil domain

4NQJ · E3 ubiquitin-protein ligase TRIM69: “Structure of coiled-coil domain”. X-ray diffraction, 4 pockets (best druggability 0.48). MolNFT v1 #101414 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4NQJ
Type: protein
Length: 530 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase TRIM69
EC: 6.3.2.-
UniProt: Q86WT6
Pockets: 4 · best druggability 0.48

Structure

x-ray diffraction · 3 distinct chains · 85% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase TRIM69 (EC 6.3.2.-)	protein	177	86% helix, 0% strand	Q86WT6
B	E3 ubiquitin-protein ligase TRIM69 (EC 6.3.2.-)	protein	176	84% helix, 1% strand	Q86WT6
C	E3 ubiquitin-protein ligase TRIM69 (EC 6.3.2.-)	protein	177	85% helix, 1% strand	Q86WT6

Ligands and binding sites

LMT · Dodecyl-beta-D-maltoside · additive · 5 copies · chains A, B, C

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

Pockets

4 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	105	0.48	0.80	21	empty
2	109	0.37	0.73	21	empty
3	111	0.35	0.73	16	empty
4	97	0.34	0.74	18	empty

Interfaces

3 interfaces between chains.

A–C · 4041 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 824 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 582 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4NQJ · Structure of coiled-coil domain · the same entry in another collection · chain A against A, TM-score 1.00
Q86WT6 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM69 (Q86WT6) · a predicted model of the same protein · chain C against A, TM-score 0.55

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 Q86WT6
Elsewhere: RCSB PDB 4NQJ · PDBe 4NQJ · UniProt Q86WT6

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