Research workbench
Crystal structure of fimh in complex with a pentaflourinated biphenyl alpha D-mannoside
Analyse Crystal structure of fimh in complex with a pentaflourinated biphenyl alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G2S
- Type
- protein
- Length
- 1,422 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type 1 fimbrin D-mannose specific adhesin
- UniProt
- P08191
- Ligands
- EJN, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I | Type 1 fimbrin D-mannose specific adhesin | protein | 158 | 6% helix, 51% strand | P08191 |
Ligands and binding sites
- EJN · (2~{R},3~{S},4~{S},5~{S},6~{R})-2-(hydroxymethyl)-6-[4-[2,3,4,5,6-pentakis(fluoranyl)phenyl]phenoxy]oxane-3, 4,5-triol · ligand · 9 copies · chains A, B, D, F, C, E, G, H, I
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.76 | 0.78 | 102 | empty |
| 2 | 1016 | 0.72 | 0.76 | 88 | SO4 |
| 3 | 632 | 0.70 | 0.78 | 66 | EJN |
| 4 | 405 | 0.63 | 0.78 | 53 | empty |
| 5 | 164 | 0.49 | 0.77 | 35 | empty |
Interfaces
12 interfaces between chains.
- C–E · 547 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 540 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 538 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 529 Ų buried · 8 hydrogen bonds · protein-protein
- E–I · 504 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6G2S · Crystal structure of FimH in complex with a pentaflourinated biphenyl alpha D-mannoside · the same entry in another collection · chain I against I, 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 F 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 6G2S · PDBe 6G2S · UniProt P08191
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