Research workbench
Crystal structure of the fimh lectin domain from E.COLI F18 in complex with trimannose
Analyse Crystal structure of the fimh lectin domain from E.COLI F18 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GTW
- Type
- protein
- Length
- 634 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fimh protein
- UniProt
- A0A0R4I961
- Ligands
- MAN, CA
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fimh protein | protein | 158 | 4% helix, 53% strand | A0A0R4I961 |
| B, D | Fimh protein | protein | 159 | 4% helix, 51% strand | A0A0R4I961 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, C, A, D
- CA · Calcium ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.69 | 0.85 | 28 | MAN |
| 2 | 240 | 0.69 | 0.85 | 29 | MAN |
| 3 | 163 | 0.55 | 0.80 | 34 | empty |
| 4 | 75 | 0.54 | 0.86 | 23 | empty |
| 5 | 187 | 0.45 | 0.74 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 596 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 585 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 321 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 321 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6GTW · Crystal structure of the FimH lectin domain from E.coli F18 in complex with trimannose · 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 A0A0R4I961
- Elsewhere: RCSB PDB 6GTW · PDBe 6GTW · UniProt A0A0R4I961
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