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A GH31 family sulfoquinovosidase from E. coli in complex with aza-sugar inhibitor IFGSQ
Analyse A GH31 family sulfoquinovosidase from E. coli in complex with aza-sugar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OHT
- Type
- protein
- Length
- 1,336 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.87
- Source
- Escherichia coli (strain K12)
- Molecule
- Sulfoquinovosidase
- EC
- 3.2.1.199
- UniProt
- P32138
- Ligands
- 9VH, CA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.87 · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfoquinovosidase (EC 3.2.1.199) | protein | 670 | 26% helix, 30% strand | P32138 |
| B | Sulfoquinovosidase (EC 3.2.1.199) | protein | 666 | 26% helix, 30% strand | P32138 |
Ligands and binding sites
- 9VH · [(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methanesulfonic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.78 | 0.89 | 39 | 9VH |
| 2 | 354 | 0.76 | 0.87 | 40 | 9VH |
| 3 | 803 | 0.69 | 0.76 | 72 | empty |
| 4 | 83 | 0.48 | 0.82 | 21 | empty |
| 5 | 75 | 0.46 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 785 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5OHT · A GH31 family sulfoquinovosidase from E. COLI in complex with aza- sugar inhibitor ifgsq · the same entry in another collection · chain A against A, TM-score 1.00
- P32138 · AlphaFold monomer V2.0 prediction for sulfoquinovosidase (P32138) · a predicted model of the same protein · chain B 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 P32138
- Elsewhere: RCSB PDB 5OHT · PDBe 5OHT · UniProt P32138
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