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Crystal structure of uracil DNA glycosylase (bdiung) from bradyrhizobium diazoefficiens

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

PDB: 5GN2
Type: protein
Length: 1,088 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BLR0248 protein
UniProt: Q89XR0
Pockets: 14 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	BLR0248 protein	protein	272	39% helix, 11% strand	Q89XR0

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	108	0.79	0.98	31	empty
2	104	0.77	0.97	30	empty
3	368	0.59	0.76	42	empty
4	283	0.58	0.78	38	empty
5	289	0.57	0.77	40	empty

Interfaces

3 interfaces between chains.

C–D · 1835 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1816 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 153 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

5GN2 · Crystal structure of Uracil DNA glycosylase (BdiUNG) from Bradyrhizobium diazoefficiens · 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 Q89XR0
Elsewhere: RCSB PDB 5GN2 · PDBe 5GN2 · UniProt Q89XR0

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