Research workbench
Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from acinetobacter baumannii complexed with NAD+ and 3-oxovalerate
Analyse Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from acinetobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZZS
- Type
- protein
- Length
- 1,547 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxybutyrate dehydrogenase
- UniProt
- A0A1E3M3N6
- Ligands
- NAD, QT8
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3-hydroxybutyrate dehydrogenase | protein | 260 | 52% helix, 14% strand | A0A1E3M3N6 |
| D | 3-hydroxybutyrate dehydrogenase | protein | 261 | 53% helix, 14% strand | A0A1E3M3N6 |
| E | 3-hydroxybutyrate dehydrogenase | protein | 254 | 54% helix, 15% strand | A0A1E3M3N6 |
| F | 3-hydroxybutyrate dehydrogenase | protein | 252 | 53% helix, 15% strand | A0A1E3M3N6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- QT8 · 3-oxidanylidenepentanoic acid · ligand · 6 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.86 | 0.87 | 58 | empty |
| 2 | 955 | 0.85 | 0.86 | 96 | NAD, QT8 |
| 3 | 238 | 0.75 | 0.89 | 30 | NAD, QT8 |
| 4 | 375 | 0.75 | 0.85 | 44 | NAD, QT8 |
| 5 | 318 | 0.74 | 0.86 | 42 | NAD |
Interfaces
9 interfaces between chains.
- C–D · 1593 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1592 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1583 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1369 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1335 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6ZZS · Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Acinetobacter baumannii… · 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 A0A1E3M3N6
- Elsewhere: RCSB PDB 6ZZS · PDBe 6ZZS · UniProt A0A1E3M3N6
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