MolNFT v1 · #114187 · protein

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

5B4U: “Crystal structure of D-3-hydroxybutyrate dehydrogenase from alcaligenes faecalis complexed with NAD+ and an…”. X-ray diffraction, 3 ligands (NAD, NA, CL), 2 pockets (best druggability 0.70). MolNFT v1 #114187 on GenesisL1: 3D…

PDB: 5B4U
Type: protein
Length: 260 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-hydroxybutyrate dehydrogenase
EC: 1.1.1.30
UniProt: D0VWQ0
Ligands: NAD, NA, CL
Pockets: 2 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	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
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion
MLA · Malonic acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	299	0.70	0.84	42	NAD, MLA
2	113	0.43	0.77	16	empty

Compared structures

5B4U · 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 5B4U · PDBe 5B4U · UniProt D0VWQ0

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