Research workbench
Crystal structure of fimh lectin domain in complex with 3-fluoro- heptylmannoside
Analyse Crystal structure of fimh lectin domain in complex with 3-fluoro… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L4W
- Type
- protein
- Length
- 474 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein fimh
- UniProt
- P08191
- Ligands
- 6KH
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein fimh | protein | 158 | 6% helix, 53% strand | P08191 |
Ligands and binding sites
- 6KH · heptyl 3-fluoro-alpha-D-mannopyranoside · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.63 | 0.78 | 33 | empty |
| 2 | 150 | 0.59 | 0.83 | 34 | empty |
| 3 | 51 | 0.25 | 0.74 | 10 | empty |
Interfaces
2 interfaces between chains.
- A–B · 547 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 115 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5L4W · Crystal structure of FimH lectin domain in complex with 3-Fluoro-Heptylmannoside · 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 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 5L4W · PDBe 5L4W · UniProt P08191
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