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Crystal structure of the human TRIM25 pryspry domain

Analyse Crystal structure of the human TRIM25 pryspry domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FLM
Type: protein
Length: 595 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 UBIQUITIN/ISG15 ligase TRIM25
EC: 6.3.2.-, 2.3.2.27
UniProt: Q14258
Ligands: SO4, CL
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	E3 UBIQUITIN/ISG15 ligase TRIM25 (EC 6.3.2.-, 2.3.2.27)	protein	198	11% helix, 41% strand	Q14258
C	E3 UBIQUITIN/ISG15 ligase TRIM25 (EC 6.3.2.-, 2.3.2.27)	protein	199	12% helix, 40% strand	Q14258

Ligands and binding sites

SO4 · Sulfate ion · ion · 13 copies · chains A, C, B
CL · Chloride ion · ion · chains C

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

Pockets

4 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	810	0.72	0.78	80	SO4
2	96	0.44	0.79	23	empty
3	51	0.35	0.79	14	empty
4	69	0.34	0.76	17	empty

Interfaces

2 interfaces between chains.

A–C · 709 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 342 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6FLM · Crystal structure of the human TRIM25 PRYSPRY domain · the same entry in another collection · chain A against A, TM-score 1.00
Q14258 · AlphaFold monomer V2.0 prediction for E3 UBIQUITIN/ISG15 ligase TRIM25 (Q14258) · a predicted model of the same protein · chain A 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 Q14258
Elsewhere: RCSB PDB 6FLM · PDBe 6FLM · UniProt Q14258

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