MolNFT v1 · #172349 · protein
Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from psychrobacter arcticus complexed with NAD+ and 3-oxovalerate
6ZZP · Putative beta-hydroxybutyrate dehydrogenase: “Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from psychrobacter arcticus complexed with NAD+ and…”. X-ray diffraction, 2 ligands (NAD, QT8), 11 pockets (best druggability…
- PDB
- 6ZZP
- Type
- protein
- Length
- 1,018 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative beta-hydroxybutyrate dehydrogenase
- EC
- 1.1.1.30
- UniProt
- Q4FRT2
- Ligands
- NAD, QT8
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 265 | 51% helix, 16% strand | Q4FRT2 |
| B | Putative beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 254 | 46% helix, 17% strand | Q4FRT2 |
| C | Putative beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 253 | 48% helix, 16% strand | Q4FRT2 |
| D | Putative beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 246 | 44% helix, 17% strand | Q4FRT2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- QT8 · 3-oxidanylidenepentanoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.74 | 0.87 | 38 | NAD, QT8 |
| 2 | 301 | 0.73 | 0.86 | 38 | NAD, QT8 |
| 3 | 356 | 0.72 | 0.84 | 38 | NAD, QT8 |
| 4 | 262 | 0.72 | 0.86 | 38 | NAD, QT8 |
| 5 | 765 | 0.70 | 0.77 | 87 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2050 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2041 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 295 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 284 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 261 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZZP · Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Psychrobacter arcticus… · 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 Q4FRT2
- Elsewhere: RCSB PDB 6ZZP · PDBe 6ZZP · UniProt Q4FRT2
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