Research workbench
Crystal structure of alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase in complex with NAD(+) and acetate
Analyse Crystal structure of alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VDQ
- 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, CA, CL
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 54% 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 | 54% helix, 13% strand | D0VWQ0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains B, D, A, C
- CL · Chloride ion · ion · 4 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.85 | 0.87 | 55 | CA |
| 2 | 324 | 0.71 | 0.84 | 40 | ACT, NAD |
| 3 | 299 | 0.70 | 0.84 | 40 | ACT, NAD |
| 4 | 317 | 0.70 | 0.84 | 39 | ACT, NAD |
| 5 | 288 | 0.70 | 0.84 | 39 | ACT, NAD |
Interfaces
6 interfaces between chains.
- B–C · 1498 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1480 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1252 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1240 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 251 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3VDQ · Crystal structure of alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase in complex… · 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 3VDQ · PDBe 3VDQ · UniProt D0VWQ0
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