MolNFT v1 · #83122 · protein

Crystal structure of D-3-hydroxybutyrate dehydrogenase from alcaligenes faecalis complexed with NAD+ and an inhibitor methylmalonate

3W8D: “Crystal structure of D-3-hydroxybutyrate dehydrogenase from alcaligenes faecalis complexed with NAD+ and an…”. X-ray diffraction, 4 ligands (NAD, DXX, NA), 1 pocket (best druggability 0.72). MolNFT v1 #83122 on GenesisL1: 3D…

PDB: 3W8D
Type: protein
Length: 260 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-3-hydroxybutyrate dehydrogenase
EC: 1.1.1.30
UniProt: D0VWQ0
Ligands: NAD, DXX, NA, CL
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	260	54% helix, 13% strand	D0VWQ0

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
DXX · Methylmalonic acid · ligand · chains A
NA · Sodium ion · metal · 3 copies · chains A
CL · Chloride ion · ion · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	474	0.72	0.82	53	NAD, DXX, CL

Compared structures

3W8D · Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis… · 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 D0VWQ0
Elsewhere: RCSB PDB 3W8D · PDBe 3W8D · UniProt D0VWQ0

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