MolNFT v1 · #178769 · protein

Crystal structure of TRIM65 pspry domain

7JL4 · Tripartite motif-containing protein 65: “Crystal structure of TRIM65 pspry domain”. X-ray diffraction, 3 pockets (best druggability 0.61). MolNFT v1 #178769 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7JL4
Type: protein
Length: 553 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tripartite motif-containing protein 65
UniProt: Q6PJ69
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tripartite motif-containing protein 65	protein	190	5% helix, 41% strand	Q6PJ69
C	Tripartite motif-containing protein 65	protein	176	7% helix, 45% strand	Q6PJ69
B	Tripartite motif-containing protein 65	protein	187	5% helix, 42% strand	Q6PJ69

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, 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	471	0.61	0.76	52	empty
2	70	0.45	0.82	14	empty
3	51	0.24	0.72	12	empty

Interfaces

3 interfaces between chains.

A–B · 322 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 90 Å² buried · 0 hydrogen bonds · protein-protein
C–B · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7JL4 · Crystal structure of TRIM65 PSpry domain · the same entry in another collection · chain A against A, TM-score 1.00
Q6PJ69 · AlphaFold monomer V2.0 prediction for tripartite motif-containing protein 65 (Q6PJ69) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q6PJ69
Elsewhere: RCSB PDB 7JL4 · PDBe 7JL4 · UniProt Q6PJ69

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