MolNFT v1 · #151138 · protein

Structure of the C-terminal domain of USP25 (748-1048)

6HEM · Ubiquitin carboxyl-terminal hydrolase 25: “Structure of the C-terminal domain of USP25 (748-1048)”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.55). MolNFT v1 #151138 on GenesisL1: 3D structure, binding sites…

PDB: 6HEM
Type: protein
Length: 300 residues
Chains: 1
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: NA
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 25 (EC 3.4.19.12)	protein	300	72% helix, 0% strand	Q9UHP3

Ligands and binding sites

NA · Sodium ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A

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	280	0.55	0.76	30	empty
2	142	0.43	0.75	24	NA
3	113	0.42	0.76	26	GOL

Compared structures

6HEM · Structure of the C-terminal domain of USP25 (748-1048) · 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 A against A, TM-score 0.96

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 6HEM · PDBe 6HEM · UniProt Q9UHP3

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