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Crystal structure of uracil-DNA glycosylase from atlantic cod (gadus morhua)

Analyse Crystal structure of uracil-DNA glycosylase from atlantic cod (gadus morhua) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OKB
Type: protein
Length: 446 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uracil-DNA glycosylase
EC: 3.2.2.3
UniProt: Q9I983
Ligands: CL
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Uracil-DNA glycosylase (EC 3.2.2.3)	protein	223	41% helix, 11% strand	Q9I983

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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	424	0.60	0.75	67	GOL
2	111	0.45	0.78	31	GOL
3	53	0.30	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 402 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1OKB · crystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua) · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9I983
Elsewhere: RCSB PDB 1OKB · PDBe 1OKB · UniProt Q9I983

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