MolNFT v1 · #103358 · protein
Crystal structure of a bacterial fucosidase with inhibitor 1-phenyl-4- [(2S,3S,4R,5S)-3,4-dihydroxy-5-methylpyrrolidin-2-YL]TRIAZOLE
4PEE · Alpha-L-fucosidase: “Crystal structure of a bacterial fucosidase with inhibitor 1-phenyl-4…”. X-ray diffraction, 2 ligands (2OX, SO4), 11 pockets (best druggability 0.70). MolNFT v1 #103358 on GenesisL1: 3D structure, binding sites…
- PDB
- 4PEE
- Type
- protein
- Length
- 1,782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- 2OX, SO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-L-fucosidase | protein | 445 | 31% helix, 22% strand | Q8A3I4 |
| C | Alpha-L-fucosidase | protein | 446 | 31% helix, 22% strand | Q8A3I4 |
| D | Alpha-L-fucosidase | protein | 446 | 31% helix, 22% strand | Q8A3I4 |
Ligands and binding sites
- 2OX · (2S,3R,4S,5S)-2-methyl-5-(1-phenyl-1H-1,2,3-triazol-4-yl)pyrrolidine-3,4-diol · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- IMD · Imidazole · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.70 | 0.75 | 70 | empty |
| 2 | 475 | 0.65 | 0.77 | 52 | empty |
| 3 | 432 | 0.64 | 0.78 | 50 | empty |
| 4 | 69 | 0.42 | 0.80 | 18 | 2OX |
| 5 | 123 | 0.40 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 379 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 361 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 107 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4PEE · Crystal structure of a bacterial fucosidase with inhibitor… · 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 4PEE · PDBe 4PEE · UniProt Q8A3I4
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