MolNFT v1 · #82149 · protein

Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+)

3VDR: “Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate…”. X-ray diffraction, 6 ligands (NAD, NAI, 3HR), 12 pockets (best druggability 0.85). MolNFT v1 #82149 on GenesisL1: 3D structure…

PDB: 3VDR
Type: protein
Length: 1,040 residues
Chains: 4
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, NAI, 3HR, AAE, CA, CL
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	D-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	260	47% helix, 13% strand	D0VWQ0

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
3HR · (3R)-3-hydroxybutanoic acid · ligand · 4 copies · chains A, B, C, D
AAE · Acetoacetic acid · ligand · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, C, B, D
CL · Chloride ion · ion · 3 copies · chains A, B, 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	898	0.85	0.87	57	CA
2	524	0.72	0.81	60	CL, NAD, NAI, 3HR, AAE
3	324	0.70	0.83	40	NAD, NAI, 3HR, AAE
4	329	0.70	0.83	40	NAD, NAI, 3HR, AAE
5	276	0.68	0.83	42	NAD, NAI, 3HR, AAE

Interfaces

6 interfaces between chains.

B–C · 1509 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 1497 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1245 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1231 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 267 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3VDR · Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the… · 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 3VDR · PDBe 3VDR · UniProt D0VWQ0

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