Research workbench
Crystal structure of the fimbrial adhesin fimh in complex with its high-mannose epitope
Analyse Crystal structure of the fimbrial adhesin fimh in complex with its high-mannose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VCO
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein fimh
- UniProt
- P08191
- Ligands
- MAN, NAG, NI, SO4
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein fimh | protein | 158 | 6% helix, 53% strand | P08191 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 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 | 82 | 0.46 | 0.82 | 21 | empty |
| 2 | 89 | 0.39 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 554 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2VCO · Crystal structure of the fimbrial adhesin FimH in complex with its high-mannose epitope · the same entry in another collection · chain A against A, TM-score 1.00
- P08191 · AlphaFold monomer V2.0 prediction for type 1 fimbrin D-mannose specific adhesin (P08191) · a predicted model of the same protein · chain B against A, TM-score 0.82
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 P08191
- Elsewhere: RCSB PDB 2VCO · PDBe 2VCO · UniProt P08191
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