MolNFT v1 · #93491 · protein
Crystal structure of a putative alpha-L-fucosidase (BT_0435) from bacteroides thetaiotaomicron vpi-5482 at 1.80 a resolution
4H41: “Crystal structure of a putative alpha-L-fucosidase (BT_0435) from bacteroides thetaiotaomicron vpi-5482 at…”. X-ray diffraction, 2 ligands (UNL, NA), 11 pockets (best druggability 0.78). MolNFT v1 #93491 on GenesisL1: 3D structure…
- PDB
- 4H41
- Type
- protein
- Length
- 961 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-L-fucosidase
- UniProt
- Q8AAM9
- Ligands
- UNL, NA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alpha-L-fucosidase | protein | 318 | 41% helix, 15% strand | Q8AAM9 |
| B | Putative alpha-L-fucosidase | protein | 322 | 41% helix, 15% strand | Q8AAM9 |
| C | Putative alpha-L-fucosidase | protein | 321 | 41% helix, 15% strand | Q8AAM9 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · chains B
- 1PE · Pentaethylene glycol · additive · 7 copies · chains A, C, B
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, C
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.78 | 0.97 | 29 | empty |
| 2 | 114 | 0.77 | 0.96 | 29 | empty |
| 3 | 107 | 0.77 | 0.96 | 27 | empty |
| 4 | 87 | 0.75 | 0.97 | 19 | empty |
| 5 | 585 | 0.74 | 0.81 | 67 | UNL, 1PE |
Interfaces
3 interfaces between chains.
- B–C · 1576 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1349 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1346 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
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 Q8AAM9
- Elsewhere: RCSB PDB 4H41 · PDBe 4H41 · UniProt Q8AAM9
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