Research workbench
Crystal structure of an alpha-L-fucosidase GH29 from bacteroides thetaiotaomicron
Analyse Crystal structure of an alpha-L-fucosidase GH29 from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WVV
- Type
- protein
- Length
- 1,764 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-fucosidase
- UniProt
- Q8A3I4
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-fucosidase | protein | 438 | 32% helix, 22% strand | Q8A3I4 |
| B | Alpha-L-fucosidase | protein | 446 | 31% helix, 22% strand | Q8A3I4 |
| C | Alpha-L-fucosidase | protein | 443 | 32% helix, 22% strand | Q8A3I4 |
| D | Alpha-L-fucosidase | protein | 437 | 32% helix, 22% strand | Q8A3I4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.72 | 0.75 | 84 | empty |
| 2 | 583 | 0.68 | 0.78 | 59 | empty |
| 3 | 489 | 0.67 | 0.78 | 52 | empty |
| 4 | 162 | 0.63 | 0.84 | 34 | TRS |
| 5 | 161 | 0.61 | 0.84 | 34 | TRS, GOL |
Interfaces
3 interfaces between chains.
- A–B · 356 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 350 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 150 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WVV · Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron · the same entry in another collection · chain C against C, 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 2WVV · PDBe 2WVV · UniProt Q8A3I4
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