Research workbench
Crystal structure of a putative D-beta-hydroxybutyrate dehydrogenase from burkholderia cenocepacia J2315 in complex with NAD
Analyse Crystal structure of a putative 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
- 8DT1
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxybutyrate dehydrogenase
- UniProt
- A0A1V2Y0M0
- Ligands
- NAD, PO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxybutyrate dehydrogenase | protein | 251 | 51% helix, 17% strand | A0A1V2Y0M0 |
| B, D | 3-hydroxybutyrate dehydrogenase | protein | 251 | 51% helix, 17% strand | A0A1V2Y0M0 |
| C | 3-hydroxybutyrate dehydrogenase | protein | 259 | 52% helix, 17% strand | A0A1V2Y0M0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · 8 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.82 | 0.94 | 32 | empty |
| 2 | 756 | 0.77 | 0.81 | 80 | NAD, CIT |
| 3 | 1196 | 0.77 | 0.79 | 115 | NAD, CIT |
| 4 | 399 | 0.62 | 0.77 | 43 | NAD, CIT |
| 5 | 77 | 0.46 | 0.82 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1712 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1688 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1299 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1286 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 73 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 8DT1 · Crystal Structure of a Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia… · 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 A0A1V2Y0M0
- Elsewhere: RCSB PDB 8DT1 · PDBe 8DT1 · UniProt A0A1V2Y0M0
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