Research workbench

TRIM7 in complex with C-terminal peptide of 2C

Analyse TRIM7 in complex with C-terminal peptide of 2C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7W0T
Type: protein
Length: 526 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase TRIM7; Peptide
EC: 2.3.2.27
UniProt: Q9C029
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 5 distinct chains · 3% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, B	E3 ubiquitin-protein ligase TRIM7 (EC 2.3.2.27)	protein	169	2% helix, 43% strand	Q9C029
C	E3 ubiquitin-protein ligase TRIM7 (EC 2.3.2.27)	protein	170	2% helix, 43% strand	Q9C029
A	Peptide	protein	7	43% helix, 0% strand	—
D	Peptide	protein	6	0% helix, 0% strand	—
E	Peptide	protein	5	60% helix, 0% strand	—

Pockets

5 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	260	0.60	0.79	40	empty
2	140	0.50	0.79	24	empty
3	95	0.36	0.75	17	empty
4	72	0.31	0.74	16	empty
5	59	0.28	0.74	14	empty

Interfaces

6 interfaces between chains.

C–B · 643 Å² buried · 7 hydrogen bonds · protein-protein
F–A · 423 Å² buried · 11 hydrogen bonds · protein-protein
C–E · 411 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 408 Å² buried · 9 hydrogen bonds · protein-protein
F–C · 276 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7W0T · TRIM7 in complex with C-terminal peptide of 2C · the same entry in another collection · chain E against E, 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 F 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 7W0T · PDBe 7W0T · UniProt Q9C029

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