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Crystal structure of fucose binding lectin from aspergillus fumigatus (afl) in complex with L-galactopyranose.
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
- 4D52
- Type
- protein
- Length
- 1,254 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-specific lectin flea
- UniProt
- Q4WW81
- Ligands
- GXL, GIV, NA, ZN
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Fucose-specific lectin flea | protein | 314 | 4% helix, 51% strand | Q4WW81 |
| C | Fucose-specific lectin flea | protein | 312 | 4% helix, 53% strand | Q4WW81 |
Ligands and binding sites
- GXL · alpha-L-galactopyranose · ligand · 14 copies · chains A, C, B, D
- GIV · beta-L-galactopyranose · ligand · 12 copies · chains A, C, B, D
- NA · Sodium ion · metal · 3 copies · chains B, C, D
- ZN · Zinc ion · metal · chains B
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.89 | 0.90 | 137 | NA |
| 2 | 1177 | 0.87 | 0.89 | 130 | NA |
| 3 | 599 | 0.65 | 0.76 | 76 | GXL, GIV |
| 4 | 235 | 0.64 | 0.82 | 34 | empty |
| 5 | 101 | 0.44 | 0.79 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1169 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1166 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 307 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 247 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 53 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 4D52 · 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 C 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 4D52 · PDBe 4D52 · UniProt Q4WW81
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