Research workbench
The crystal structure of D-beta-hydroxybutyrate dehydrogenase from sinorhizobium meliloti
Analyse The crystal structure of D-beta-hydroxybutyrate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V2H
- Type
- protein
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-beta-hydroxybutyrate dehydrogenase
- EC
- 1.1.1.30
- UniProt
- O86034
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 232 | 50% helix, 16% strand | O86034 |
| B | D-beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 231 | 49% helix, 16% strand | O86034 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.54 | 0.76 | 36 | empty |
| 2 | 265 | 0.53 | 0.76 | 37 | empty |
| 3 | 53 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1365 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3V2H · The crystal structure of D-beta-hydroxybutyrate dehydrogenase from Sinorhizobium meliloti · the same entry in another collection · chain B against B, TM-score 1.00
- O86034 · AlphaFold monomer V2.0 prediction for D-beta-hydroxybutyrate dehydrogenase (O86034) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O86034
- Elsewhere: RCSB PDB 3V2H · PDBe 3V2H · UniProt O86034
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