Research workbench
Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S, 4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine
Analyse Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I5R
- Type
- protein
- Length
- 1,761 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- 68F, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Alpha-L-fucosidase | protein | 440 | 32% helix, 23% strand | Q8A3I4 |
| C | Alpha-L-fucosidase | protein | 441 | 32% helix, 22% strand | Q8A3I4 |
Ligands and binding sites
- 68F · (2S,3S,4R,5S,2'S,3'S,4'R,5'S)-2,2'-(butane-1,4-diyl)bis(5-methylpyrrolidine-3,4-diol) · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.70 | 0.75 | 71 | empty |
| 2 | 558 | 0.66 | 0.77 | 55 | empty |
| 3 | 394 | 0.63 | 0.78 | 51 | empty |
| 4 | 61 | 0.41 | 0.80 | 17 | 68F |
| 5 | 64 | 0.41 | 0.80 | 17 | 68F |
Interfaces
3 interfaces between chains.
- C–D · 383 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 329 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 107 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5I5R · Crystal structure of a bacterial fucosidase with iminocyclitol… · 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 Q8A3I4
- Elsewhere: RCSB PDB 5I5R · PDBe 5I5R · UniProt Q8A3I4
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