Research workbench
Crystal structure of sulfoacetaldehyde reductase from Bifidobacterium kashiwanohense
Analyse Crystal structure of sulfoacetaldehyde reductase from Bifidobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JKO
- Type
- protein
- Length
- 1,504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Bifidobacterium kashiwanohense PV20-2
- Molecule
- Methanol dehydrogenase
- UniProt
- A0A0A7I0A5
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Methanol dehydrogenase | protein | 376 | 57% helix, 11% strand | A0A0A7I0A5 |
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
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.80 | 0.82 | 100 | empty |
| 2 | 730 | 0.73 | 0.79 | 55 | empty |
| 3 | 539 | 0.73 | 0.81 | 60 | empty |
| 4 | 969 | 0.72 | 0.76 | 81 | empty |
| 5 | 446 | 0.69 | 0.80 | 55 | empty |
Interfaces
5 interfaces between chains.
- A–C · 683 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 511 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 253 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 173 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JKO · Crystal structure of sulfoacetaldehyde reductase from bifidobacterium kashiwanohense · 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 A0A0A7I0A5
- Elsewhere: RCSB PDB 6JKO · PDBe 6JKO · UniProt A0A0A7I0A5
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