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Crystal structure of an oxidoreductase from brucella ovis

Analyse Crystal structure of an oxidoreductase from brucella ovis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ER6
Type: protein
Length: 969 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family
UniProt: A0A0H3ATY4
Pockets: 10 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family	protein	251	50% helix, 15% strand	A0A0H3ATY4
B	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family	protein	241	49% helix, 16% strand	A0A0H3ATY4
C	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family	protein	238	50% helix, 16% strand	A0A0H3ATY4
D	Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family	protein	239	49% helix, 15% strand	A0A0H3ATY4

Ligands and binding sites

ACT · Acetate ion · additive · 8 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	762	0.87	0.90	68	EDO
2	787	0.72	0.77	79	empty
3	303	0.59	0.77	43	empty
4	297	0.58	0.77	39	empty
5	252	0.56	0.77	47	ACT

Interfaces

6 interfaces between chains.

C–D · 1666 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 1658 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 1473 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 1462 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 277 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5ER6 · Crystal structure of an oxidoreductase from Brucella ovis · 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 A0A0H3ATY4
Elsewhere: RCSB PDB 5ER6 · PDBe 5ER6 · UniProt A0A0H3ATY4

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