MolNFT v1 · #189860 · protein

TRIM7 in complex with C-terminal peptide of 2C

7W0S · E3 ubiquitin-protein ligase TRIM7: “TRIM7 in complex with C-terminal peptide of 2C”. X-ray diffraction, 1 ligand (NO3), 3 pockets (best druggability 0.62). MolNFT v1 #189860 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7W0S
Type: protein
Length: 520 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
Ligands: NO3
Pockets: 3 · best druggability 0.62

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, C, E	E3 ubiquitin-protein ligase TRIM7 (EC 2.3.2.27)	protein	169	4% helix, 43% strand	Q9C029
A, F	Peptide	protein	4	0% helix, 0% strand	—
D	Peptide	protein	5	60% helix, 0% strand	—

Ligands and binding sites

NO3 · Nitrate ion · ion · 8 copies · chains B, C, E
GOL · Glycerol · additive · 4 copies · chains B, E
PEG · Di(hydroxyethyl)ether · additive · chains C

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

Pockets

3 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	250	0.62	0.81	35	empty
2	163	0.44	0.75	31	GOL
3	95	0.38	0.76	19	empty

Interfaces

5 interfaces between chains.

B–C · 627 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 389 Å² buried · 9 hydrogen bonds · protein-protein
B–A · 348 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 345 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 286 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7W0S · TRIM7 in complex with C-terminal peptide of 2C · the same entry in another collection · chain C against C, 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 7W0S · PDBe 7W0S · UniProt Q9C029

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