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Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase

Analyse Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WMB
Type: protein
Length: 520 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D(-)-3-hydroxybutyrate dehydrogenase
EC: 1.1.1.30
UniProt: Q5KST5
Ligands: MG
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	260	54% helix, 14% strand	Q5KST5

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
CAC · Cacodylate ion · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	425	0.67	0.79	46	CAC
2	408	0.66	0.79	42	CAC
3	125	0.42	0.76	21	empty
4	118	0.37	0.74	22	empty

Interfaces

1 interface between chains.

A–B · 1251 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1WMB · Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase · 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 Q5KST5
Elsewhere: RCSB PDB 1WMB · PDBe 1WMB · UniProt Q5KST5

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