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Crystal structure of the fimh lectin domain from E.COLI K12 in complex with the dimannoside MAN(ALPHA1-2)MAN
Analyse Crystal structure of the fimh lectin domain from E.COLI K12 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GTX
- Type
- protein
- Length
- 632 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type 1 fimbrin D-mannose specific adhesin
- UniProt
- P08191
- Ligands
- MMA, MAN, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Type 1 fimbrin D-mannose specific adhesin | protein | 158 | 6% helix, 53% strand | P08191 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.72 | 0.84 | 60 | empty |
| 2 | 322 | 0.67 | 0.82 | 50 | empty |
| 3 | 138 | 0.66 | 0.88 | 27 | empty |
| 4 | 132 | 0.46 | 0.78 | 21 | empty |
| 5 | 51 | 0.40 | 0.82 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–D · 659 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 654 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 617 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 355 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 173 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6GTX · Crystal structure of the FimH lectin domain from E.coli K12 in complex with the… · the same entry in another collection · chain D against D, 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 C 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 6GTX · PDBe 6GTX · UniProt P08191
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