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Crystal structure of a D-beta-hydroxybutyrate dehydrogenase from burkholderia multivorans
Analyse Crystal structure of a D-beta-hydroxybutyrate dehydrogenase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UNL
- Type
- protein
- Length
- 1,054 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-ketoacyl-acp reductase
- UniProt
- A0A1B4TPS8
- Ligands
- NO3
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | 3-ketoacyl-acp reductase | protein | 264 | 47% helix, 14% strand | A0A1B4TPS8 |
| B | 3-ketoacyl-acp reductase | protein | 262 | 47% helix, 15% strand | A0A1B4TPS8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.85 | 0.85 | 75 | empty |
| 2 | 216 | 0.78 | 0.92 | 29 | EDO |
| 3 | 304 | 0.76 | 0.88 | 40 | empty |
| 4 | 308 | 0.75 | 0.87 | 46 | NO3 |
| 5 | 324 | 0.75 | 0.86 | 43 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1687 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1662 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1520 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1478 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 157 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5UNL · Crystal structure of a D-beta-hydroxybutyrate dehydrogenase from Burkholderia multivorans · 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 A0A1B4TPS8
- Elsewhere: RCSB PDB 5UNL · PDBe 5UNL · UniProt A0A1B4TPS8
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