MolNFT v1 · #120034 · protein

Structure of selenomethionine-labelled uracil DNA glycosylase (bdiung) from bradyrhizobium diazoefficiens

5GN3 · BLR0248 protein: “Structure of selenomethionine-labelled uracil DNA glycosylase (bdiung) from bradyrhizobium diazoefficiens”. X-ray diffraction, 14 pockets (best druggability 0.78). MolNFT v1 #120034 on GenesisL1: 3D structure…

PDB: 5GN3
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 0.78

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	BLR0248 protein	protein	272	38% helix, 12% strand	Q89XR0

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	112	0.78	0.97	35	empty
2	95	0.77	0.98	26	empty
3	292	0.55	0.76	32	empty
4	289	0.55	0.76	39	empty
5	279	0.55	0.77	39	empty

Interfaces

3 interfaces between chains.

A–B · 1841 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1838 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 154 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

5GN3 · Structure of selenomethionine-labelled Uracil DNA glycosylase (BdiUNG) from… · 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 5GN3 · PDBe 5GN3 · UniProt Q89XR0

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