Research workbench
Structure of the FimH lectin domain in the trigonal space group, in complex with a methyl ester octyl alpha-D-mannoside at 2.4 A resolution
Analyse Structure of the FimH lectin domain in the trigonal space group, in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AVI
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- ESCHERICHIA COLI
- Molecule
- Fimh
- UniProt
- A2IC68
- Ligands
- XNS, NI, SO4
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fimh | protein | 158 | 6% helix, 53% strand | A2IC68 |
Ligands and binding sites
- XNS · Methyl ester octyl alpha-1O-D-mannopyrannoside · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.37 | 0.76 | 23 | SO4 |
| 2 | 70 | 0.33 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 543 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4AVI · Structure of the fimh lectin domain in the trigonal space group, in complex with a methyl… · 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 A2IC68
- Elsewhere: RCSB PDB 4AVI · PDBe 4AVI · UniProt A2IC68
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