Research workbench
Crystal structure of acetoin dehydrogenase yohf from salmonella typhimurium
Analyse Crystal structure of acetoin dehydrogenase yohf from salmonella typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WON
- Type
- protein
- Length
- 1,946 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yohf
- EC
- 1.-.-.-
- UniProt
- Q8ZNM5
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yohf (EC 1.-.-.-) | protein | 241 | 46% helix, 17% strand | Q8ZNM5 |
| B, C | Yohf (EC 1.-.-.-) | protein | 244 | 48% helix, 17% strand | Q8ZNM5 |
| D | Yohf (EC 1.-.-.-) | protein | 241 | 47% helix, 17% strand | Q8ZNM5 |
| E | Yohf (EC 1.-.-.-) | protein | 239 | 48% helix, 17% strand | Q8ZNM5 |
| F | Yohf (EC 1.-.-.-) | protein | 243 | 47% helix, 17% strand | Q8ZNM5 |
| G | Yohf (EC 1.-.-.-) | protein | 253 | 45% helix, 16% strand | Q8ZNM5 |
| H | Yohf (EC 1.-.-.-) | protein | 241 | 46% helix, 17% strand | Q8ZNM5 |
Ligands and binding sites
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 | 1175 | 0.84 | 0.85 | 77 | empty |
| 2 | 1172 | 0.84 | 0.85 | 111 | empty |
| 3 | 938 | 0.80 | 0.82 | 90 | empty |
| 4 | 412 | 0.77 | 0.87 | 52 | empty |
| 5 | 390 | 0.65 | 0.79 | 51 | empty |
Interfaces
15 interfaces between chains.
- G–H · 1681 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1679 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1675 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1666 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1491 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6WON · Crystal structure of acetoin dehydrogenase YohF from Salmonella typhimurium · 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 Q8ZNM5
- Elsewhere: RCSB PDB 6WON · PDBe 6WON · UniProt Q8ZNM5
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