Research workbench
Crystal structure of L-2,3-butanediol dehydrogenase
Analyse Crystal structure of L-2,3-butanediol dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A28
- Type
- protein
- Length
- 2,056 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-2.3-butanediol dehydrogenase
- UniProt
- Q9ZNN8
- Ligands
- NAD, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A, B, E, F, G, H | L-2.3-butanediol dehydrogenase | protein | 257 | 54% helix, 15% strand | Q9ZNN8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains C, D, A, B, E, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains C, B, D, A, E, H, F, G
- BME · Beta-mercaptoethanol · additive · 8 copies · chains C, D, A, B, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.77 | 0.80 | 84 | NAD, BME |
| 2 | 890 | 0.76 | 0.79 | 86 | NAD, BME |
| 3 | 310 | 0.75 | 0.87 | 43 | NAD, BME |
| 4 | 339 | 0.74 | 0.86 | 44 | NAD, BME |
| 5 | 343 | 0.74 | 0.85 | 45 | NAD, BME |
Interfaces
14 interfaces between chains.
- A–B · 1694 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1678 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1657 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1645 Ų buried · 14 hydrogen bonds · protein-protein
- D–A · 1490 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 Q9ZNN8
- Elsewhere: RCSB PDB 3A28 · PDBe 3A28 · UniProt Q9ZNN8
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