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Crystal structure of fucose binding lectin from aspergillus fumigatus (afl) in complex with B-methylfucoside
Analyse Crystal structure of fucose binding lectin from aspergillus fumigatus (afl) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C1Y
- Type
- protein
- Length
- 1,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-specific lectin flea
- UniProt
- Q4WW81
- Ligands
- MFB, CA
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-specific lectin flea | protein | 314 | 5% helix, 51% strand | Q4WW81 |
Ligands and binding sites
- MFB · methyl beta-L-fucopyranoside · ligand · 12 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.89 | 0.90 | 141 | GOL |
| 2 | 1179 | 0.85 | 0.86 | 125 | empty |
| 3 | 468 | 0.75 | 0.84 | 53 | empty |
| 4 | 550 | 0.61 | 0.74 | 62 | MFB |
| 5 | 93 | 0.37 | 0.75 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1170 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1153 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 133 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4C1Y · Crystal Structure of Fucose binding lectin from Aspergillus Fumigatus (AFL) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q4WW81 · AlphaFold monomer V2.0 prediction for fucose-specific lectin (Q4WW81) · a predicted model of the same protein · 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 Q4WW81
- Elsewhere: RCSB PDB 4C1Y · PDBe 4C1Y · UniProt Q4WW81
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