Research workbench

E3 ring ligase binding domain with peptide

Analyse E3 ring ligase binding domain with peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OW2
Type: protein
Length: 709 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase TRIM7; E3 ubiquitin-protein ligase RNF187 peptide
EC: 2.3.2.27
UniProt: Q9C029
Ligands: CL, PO4
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	E3 ubiquitin-protein ligase TRIM7 (EC 2.3.2.27)	protein	171	4% helix, 42% strand	Q9C029
B	E3 ubiquitin-protein ligase TRIM7 (EC 2.3.2.27)	protein	168	0% helix, 43% strand	Q9C029
E, F, G, H	E3 ubiquitin-protein ligase RNF187 peptide (EC 2.3.2.27)	protein	7	71% helix, 0% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, D
PO4 · Phosphate ion · ion · chains D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	929	0.74	0.78	123	CL
2	182	0.48	0.75	24	empty
3	139	0.48	0.78	22	empty
4	150	0.45	0.75	24	empty
5	136	0.43	0.75	24	empty

Interfaces

14 interfaces between chains.

A–B · 399 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 385 Å² buried · 2 hydrogen bonds · protein-protein
A–E · 383 Å² buried · 9 hydrogen bonds · protein-protein
C–G · 374 Å² buried · 8 hydrogen bonds · protein-protein
D–H · 373 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7OW2 · E3 RING ligase binding domain with peptide · the same entry in another collection · chain H against H, TM-score 1.00
Q9C029 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM7 (Q9C029) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q9C029
Elsewhere: RCSB PDB 7OW2 · PDBe 7OW2 · UniProt Q9C029

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.