Research workbench
The binary complex of D-3-hydroxybutyrate dehydrogenase with NAD+
Analyse The binary complex of D-3-hydroxybutyrate dehydrogenase with NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZTV
- Type
- protein
- Length
- 1,014 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D(-)-3-hydroxybutyrate dehydrogenase
- EC
- 1.1.1.30
- UniProt
- Q5KST5
- Ligands
- NAD, MG
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 260 | 52% helix, 13% strand | Q5KST5 |
| B | D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 246 | 49% helix, 15% strand | Q5KST5 |
| C | D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 255 | 53% helix, 15% strand | Q5KST5 |
| D | D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 253 | 53% helix, 15% strand | Q5KST5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.85 | 0.87 | 56 | empty |
| 2 | 318 | 0.70 | 0.84 | 41 | NAD |
| 3 | 452 | 0.68 | 0.79 | 39 | NAD |
| 4 | 416 | 0.66 | 0.79 | 41 | NAD |
| 5 | 477 | 0.65 | 0.77 | 47 | NAD |
Interfaces
6 interfaces between chains.
- A–C · 1502 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1497 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1248 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1245 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 252 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2ZTV · The binary complex of D-3-hydroxybutyrate dehydrogenase with NAD+ · 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 Q5KST5
- Elsewhere: RCSB PDB 2ZTV · PDBe 2ZTV · UniProt Q5KST5
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