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Crystal structure of alpha-L-fucosidase from fusarium graminearum in the open form in complex with L-fucose
Analyse Crystal structure of alpha-L-fucosidase from fusarium graminearum in the open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PSR
- Type
- protein
- Length
- 1,164 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-fucosidase GH29
- UniProt
- J9UN47
- Ligands
- NAG, MAN, BMA, FUL, NA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-fucosidase GH29 | protein | 581 | 25% helix, 22% strand | J9UN47 |
| B | Alpha-fucosidase GH29 | protein | 583 | 26% helix, 22% strand | J9UN47 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
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 | 1020 | 0.78 | 0.80 | 105 | empty |
| 2 | 1195 | 0.77 | 0.79 | 111 | empty |
| 3 | 290 | 0.60 | 0.78 | 34 | GOL, FUL |
| 4 | 340 | 0.60 | 0.77 | 38 | GOL, FUL |
| 5 | 158 | 0.53 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 834 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 4PSR · Crystal Structure of alpha-L-fucosidase from Fusarium graminearum in the open form in… · 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 J9UN47
- Elsewhere: RCSB PDB 4PSR · PDBe 4PSR · UniProt J9UN47
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