MolNFT v1 · #152320 · protein
X-ray crystal structure of 2R,3R-butanediol dehydrogenase from bacillus subtilis
6IE0 · (R,R)-butanediol dehydrogenase: “X-ray crystal structure of 2R,3R-butanediol dehydrogenase from bacillus subtilis”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.74). MolNFT v1 #152320 on GenesisL1: 3D structure…
- PDB
- 6IE0
- Type
- protein
- Length
- 1,388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (R,R)-butanediol dehydrogenase
- EC
- 1.1.1.4
- UniProt
- O34788
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | (R,R)-butanediol dehydrogenase (EC 1.1.1.4) | protein | 347 | 29% helix, 28% strand | O34788 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.74 | 0.80 | 62 | ZN |
| 2 | 649 | 0.74 | 0.80 | 63 | empty |
| 3 | 716 | 0.73 | 0.79 | 68 | ZN |
| 4 | 661 | 0.71 | 0.78 | 69 | empty |
| 5 | 338 | 0.52 | 0.73 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1212 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1205 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 815 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 810 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 167 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6IE0 · X-ray crystal structure of 2R,3R-butanediol dehydrogenase from Bacillus subtilis · the same entry in another collection · chain D against D, TM-score 1.00
- O34788 · AlphaFold monomer V2.0 prediction for (R,R)-butanediol dehydrogenase (O34788) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O34788
- Elsewhere: RCSB PDB 6IE0 · PDBe 6IE0 · UniProt O34788
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