Research workbench
Functional annotation of salmonella enterica yihs-encoded protein
Analyse Functional annotation of salmonella enterica yihs-encoded protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZBL
- Type
- protein
- Length
- 2,499 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative isomerase
- UniProt
- Q8ZKT7
- Ligands
- BMA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Putative isomerase | protein | 416 | 50% helix, 10% strand | Q8ZKT7 |
| B | Putative isomerase | protein | 418 | 50% helix, 10% strand | Q8ZKT7 |
| C | Putative isomerase | protein | 417 | 50% helix, 10% strand | Q8ZKT7 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.84 | 0.92 | 61 | empty |
| 2 | 997 | 0.81 | 0.82 | 80 | empty |
| 3 | 373 | 0.79 | 0.88 | 36 | empty |
| 4 | 67 | 0.74 | 0.99 | 23 | BMA |
| 5 | 62 | 0.74 | 0.99 | 24 | BMA |
Interfaces
12 interfaces between chains.
- B–C · 751 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 742 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 734 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 729 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 725 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2ZBL · Functional annotation of Salmonella enterica yihS-encoded protein · the same entry in another collection · chain F against F, TM-score 1.00
- Q8ZKT7 · AlphaFold monomer V2.0 prediction for sulfoquinovose isomerase (Q8ZKT7) · a predicted model of the same protein · chain A 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 Q8ZKT7
- Elsewhere: RCSB PDB 2ZBL · PDBe 2ZBL · UniProt Q8ZKT7
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