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Structure of D-3-hydroxybutyrate dehydrogenase from pseudomonas putida

Analyse Structure of D-3-hydroxybutyrate dehydrogenase from pseudomonas putida in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Q2Q
Type: protein
Length: 1,978 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-D-hydroxybutyrate dehydrogenase
EC: 1.1.1.30
UniProt: Q9AE70
Ligands: NAD
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 8 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-D-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	250	49% helix, 15% strand	Q9AE70
B	Beta-D-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	252	49% helix, 16% strand	Q9AE70
C	Beta-D-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	243	46% helix, 16% strand	Q9AE70
D	Beta-D-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	255	51% helix, 15% strand	Q9AE70
E	Beta-D-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	249	50% helix, 15% strand	Q9AE70
F	Beta-D-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	238	48% helix, 16% strand	Q9AE70
G	Beta-D-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	251	48% helix, 14% strand	Q9AE70
H	Beta-D-hydroxybutyrate dehydrogenase (EC 1.1.1.30)	protein	240	49% helix, 15% strand	Q9AE70

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains C, D, E, F, G, A, H

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	875	0.87	0.89	56	empty
2	784	0.74	0.79	68	NAD
3	836	0.74	0.78	76	empty
4	333	0.73	0.85	40	NAD
5	295	0.71	0.85	44	NAD

Interfaces

11 interfaces between chains.

B–C · 1498 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 1488 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1231 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1229 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 1223 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

2Q2Q · Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida · 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 Q9AE70
Elsewhere: RCSB PDB 2Q2Q · PDBe 2Q2Q · UniProt Q9AE70

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