MolNFT v1 · #150799 · protein

USP25 catalytic domain

6H4J · Ubiquitin carboxyl-terminal hydrolase 25: “USP25 catalytic domain”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.74). MolNFT v1 #150799 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6H4J
Type: protein
Length: 952 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase 25
EC: 3.4.19.12
UniProt: Q9UHP3
Ligands: CL
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 25 (EC 3.4.19.12)	protein	488	40% helix, 21% strand	Q9UHP3
B	Ubiquitin carboxyl-terminal hydrolase 25 (EC 3.4.19.12)	protein	464	39% helix, 22% strand	Q9UHP3

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	497	0.74	0.82	50	empty
2	471	0.72	0.81	49	empty
3	368	0.63	0.78	36	empty
4	275	0.60	0.79	32	CL
5	363	0.60	0.77	39	empty

Interfaces

1 interface between chains.

A–B · 231 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6H4J · Usp25 catalytic domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9UHP3 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 25 (Q9UHP3) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 Q9UHP3
Elsewhere: RCSB PDB 6H4J · PDBe 6H4J · UniProt Q9UHP3

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