Research workbench
Cryatal structure analysis of meso-2,3-butanediol dehydrogenase
Analyse Cryatal structure analysis of meso-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
- 1GEG
- Type
- protein
- Length
- 2,041 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoin reductase
- EC
- 1.1.1.5
- UniProt
- Q48436
- Ligands
- NAD, GLC, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G, H | Acetoin reductase (EC 1.1.1.5) | protein | 255 | 53% helix, 16% strand | Q48436 |
| E | Acetoin reductase (EC 1.1.1.5) | protein | 256 | 53% helix, 16% strand | Q48436 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains A, B, G, H
- BME · Beta-mercaptoethanol · additive · 8 copies · chains A, B, C, D, 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 | 563 | 0.85 | 0.91 | 69 | empty |
| 2 | 822 | 0.82 | 0.85 | 90 | empty |
| 3 | 337 | 0.75 | 0.86 | 45 | NAD, BME |
| 4 | 293 | 0.74 | 0.87 | 47 | empty |
| 5 | 329 | 0.74 | 0.85 | 47 | NAD, BME |
Interfaces
15 interfaces between chains.
- C–D · 1609 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1609 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1607 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1597 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1545 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1GEG · Cryatal structure analysis of meso-2,3-butanediol dehydrogenase · the same entry in another collection · chain H against H, TM-score 1.00
- Q48436 · AlphaFold monomer V2.0 prediction for diacetyl reductase [(S)-acetoin forming] (Q48436) · a predicted model of the same protein · chain F 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 Q48436
- Elsewhere: RCSB PDB 1GEG · PDBe 1GEG · UniProt Q48436
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