MolNFT v1 · #41247 · protein

Crystal structure of uracil DNA-glycosylase from vibrio cholerae

2JHQ: “Crystal structure of uracil DNA-glycosylase from vibrio cholerae”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.52). MolNFT v1 #41247 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2JHQ
Type: protein
Length: 223 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uracil DNA-glycosylase
EC: 3.2.2.3
UniProt: Q9KPK8
Ligands: CL
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uracil DNA-glycosylase (EC 3.2.2.3)	protein	223	40% helix, 11% strand	Q9KPK8

Ligands and binding sites

CL · Chloride ion · ion · chains A

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

Pockets

2 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	192	0.52	0.77	28	CL
2	78	0.38	0.77	11	empty

Compared structures

2JHQ · Crystal structure of Uracil DNA-glycosylase from Vibrio cholerae · the same entry in another collection · chain A against A, TM-score 1.00
Q9KPK8 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (Q9KPK8) · 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 Q9KPK8
Elsewhere: RCSB PDB 2JHQ · PDBe 2JHQ · UniProt Q9KPK8

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