Research workbench
Closed conformation of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ and L-3-hydroxybutyrate
Analyse Closed conformation 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
- 2ZTL
- Type
- protein
- Length
- 1,040 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, 3HL, MG
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D(-)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) | protein | 260 | 54% helix, 13% strand | Q5KST5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- 3HL · (3S)-3-hydroxybutanoic acid · 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 | 874 | 0.86 | 0.88 | 61 | empty |
| 2 | 581 | 0.72 | 0.80 | 64 | NAD, 3HL |
| 3 | 349 | 0.71 | 0.83 | 42 | NAD, 3HL |
| 4 | 301 | 0.70 | 0.84 | 39 | NAD, 3HL |
| 5 | 274 | 0.69 | 0.84 | 39 | NAD, 3HL |
Interfaces
6 interfaces between chains.
- A–C · 1508 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1498 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1242 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1237 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 229 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2ZTL · Closed conformation of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ and… · the same entry in another collection · chain B against B, 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 2ZTL · PDBe 2ZTL · UniProt Q5KST5
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