MolNFT v1 · #120746 · protein

Crystal structure of an NAD-bound oxidoreductase from brucella ovis

5HA5 · Brucella ovis oxidoreductase: “Crystal structure of an NAD-bound oxidoreductase from brucella ovis”. X-ray diffraction, 1 ligand (NAD), 12 pockets (best druggability 0.87). MolNFT v1 #120746 on GenesisL1: 3D structure, binding sites…

PDB: 5HA5
Type: protein
Length: 972 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Brucella ovis oxidoreductase
UniProt: N8N848
Ligands: NAD
Pockets: 12 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Brucella ovis oxidoreductase	protein	250	50% helix, 15% strand	N8N848
B	Brucella ovis oxidoreductase	protein	240	49% helix, 16% strand	N8N848
C	Brucella ovis oxidoreductase	protein	238	50% helix, 16% strand	N8N848
D	Brucella ovis oxidoreductase	protein	244	48% helix, 16% strand	N8N848

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains B, C, D
EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, D, C
IMD · Imidazole · additive · 4 copies · chains A, B, C, D

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

Pockets

12 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	778	0.87	0.89	66	EDO
2	451	0.74	0.83	50	NAD
3	500	0.69	0.80	48	EDO
4	431	0.69	0.80	43	NAD, EDO
5	342	0.62	0.78	40	NAD, EDO

Interfaces

6 interfaces between chains.

C–D · 1665 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1660 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 1449 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1435 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 310 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5HA5 · Crystal structure of an NAD-bound 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 N8N848
Elsewhere: RCSB PDB 5HA5 · PDBe 5HA5 · UniProt N8N848

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