Research workbench
Structural insight into the giant calcium-binding adhesin siie: implications for the adhesion of salmonella enterica to polarized epithelial cells
Analyse Structural insight into the giant calcium-binding adhesin siie: implications… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YN3
- Type
- protein
- Length
- 1,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative inner membrane protein
- UniProt
- Q8ZKG6
- Ligands
- CA, IOD, PO4
- Pockets
- 12 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative inner membrane protein | protein | 273 | 2% helix, 51% strand | Q8ZKG6 |
| B | Putative inner membrane protein | protein | 246 | 2% helix, 51% strand | Q8ZKG6 |
| C | Putative inner membrane protein | protein | 284 | 2% helix, 50% strand | Q8ZKG6 |
| D | Putative inner membrane protein | protein | 208 | 1% helix, 48% strand | Q8ZKG6 |
Ligands and binding sites
- CA · Calcium ion · metal · 13 copies · chains A, C, B, D
- IOD · Iodide ion · ion · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.56 | 0.79 | 34 | IOD |
| 2 | 389 | 0.54 | 0.73 | 56 | empty |
| 3 | 287 | 0.51 | 0.74 | 35 | PO4 |
| 4 | 295 | 0.50 | 0.73 | 34 | empty |
| 5 | 60 | 0.49 | 0.85 | 21 | IOD |
Interfaces
4 interfaces between chains.
- A–C · 1757 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 703 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 685 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 160 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2YN3 · Structural insight into the giant calcium-binding adhesin SiiE: implications for the… · 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 Q8ZKG6
- Elsewhere: RCSB PDB 2YN3 · PDBe 2YN3 · UniProt Q8ZKG6
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