Research workbench
T190A mutant of D-3-hydroxybutyrate dehydrogenase complexed with NAD+
Analyse T190A mutant of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZTU
- Type
- protein
- Length
- 925 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 · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 235 | 48% helix, 15% strand | Q5KST5 |
| B | D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 207 | 47% helix, 12% strand | Q5KST5 |
| C | D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 242 | 51% helix, 16% strand | Q5KST5 |
| D | D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 241 | 51% helix, 15% strand | Q5KST5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.85 | 0.87 | 58 | MG |
| 2 | 267 | 0.55 | 0.76 | 34 | NAD |
| 3 | 269 | 0.54 | 0.76 | 38 | NAD |
| 4 | 226 | 0.49 | 0.75 | 39 | empty |
| 5 | 177 | 0.48 | 0.76 | 32 | NAD |
Interfaces
6 interfaces between chains.
- A–C · 1497 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1493 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1242 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1241 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 239 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2ZTU · T190A mutant of D-3-hydroxybutyrate dehydrogenase complexed 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 2ZTU · PDBe 2ZTU · UniProt Q5KST5
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