MolNFT v1 · #103308 · protein
Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S, 4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine
4PCT · Alpha-L-fucosidase: “Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S…”. X-ray diffraction, 2 ligands (H76, SO4), 9 pockets (best druggability 0.69). MolNFT v1 #103308 on GenesisL1: 3D structure, binding sites…
- PDB
- 4PCT
- Type
- protein
- Length
- 1,752 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- EC
- 3.2.1.51
- UniProt
- Q8A3I4
- Ligands
- H76, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-L-fucosidase (EC 3.2.1.51) | protein | 438 | 32% helix, 22% strand | Q8A3I4 |
| B | Alpha-L-fucosidase (EC 3.2.1.51) | protein | 439 | 32% helix, 22% strand | Q8A3I4 |
| D | Alpha-L-fucosidase (EC 3.2.1.51) | protein | 437 | 32% helix, 22% strand | Q8A3I4 |
Ligands and binding sites
- H76 · (2S,3S,4R,5S)-2-ethynyl-5-methylpyrrolidine-3,4-diol · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.69 | 0.75 | 74 | empty |
| 2 | 530 | 0.65 | 0.77 | 62 | empty |
| 3 | 379 | 0.58 | 0.75 | 46 | empty |
| 4 | 102 | 0.55 | 0.84 | 17 | empty |
| 5 | 62 | 0.40 | 0.80 | 18 | H76 |
Interfaces
3 interfaces between chains.
- C–D · 288 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 244 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 102 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4PCT · 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 4PCT · PDBe 4PCT · UniProt Q8A3I4
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