Research workbench

TRIM23 ring domain in complex with UBCH5-ub

Analyse TRIM23 ring domain in complex with UBCH5-ub in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VZW
Type: protein
Length: 601 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 D2; Ubiquitin; E3 ubiquitin-protein ligase TRIM23
EC: 2.3.2.23, 2.3.2.24
UniProt: P62837, P0CG47, P36406
Ligands: ZN
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24)	protein	146	37% helix, 19% strand	P62837
C	Ubiquitin	protein	78	19% helix, 36% strand	P0CG47
F, G	E3 ubiquitin-protein ligase TRIM23	protein	77	26% helix, 21% strand	P36406
D	Ubiquitin	protein	77	19% helix, 36% strand	P0CG47

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains F, G

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	193	0.73	0.90	37	empty
2	121	0.66	0.89	23	empty
3	72	0.57	0.88	20	empty
4	111	0.50	0.81	20	empty
5	129	0.46	0.78	16	empty

Interfaces

9 interfaces between chains.

C–B · 960 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 952 Å² buried · 20 hydrogen bonds · protein-protein
F–G · 787 Å² buried · 7 hydrogen bonds · protein-protein
G–B · 529 Å² buried · 5 hydrogen bonds · protein-protein
A–F · 527 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 isopeptide (isopeptide).

Compared structures

5VZW · TRIM23 RING domain in complex with UbcH5-Ub · the same entry in another collection · chain D against D, TM-score 1.00
P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.97
P36406 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM23 (P36406) · a predicted model of the same protein · chain F against A, TM-score 0.97

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 P62837
Every structure of UniProt P0CG47
Every structure of UniProt P36406
Elsewhere: RCSB PDB 5VZW · PDBe 5VZW · UniProt P62837 · UniProt P0CG47 · UniProt P36406

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