Research workbench
Identification of the glycan target of the nematotoxic fungal galectin CGL2 in caenorhabditis elegans
Analyse Identification of the glycan target of the nematotoxic fungal galectin CGL2 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WKK
- Type
- protein
- Length
- 600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-2
- UniProt
- Q9P4R8
- Ligands
- FUC, GAL, NAG, MG
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Galectin-2 | protein | 150 | 0% helix, 48% strand | Q9P4R8 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies
- MG · Magnesium ion · metal · chains C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.63 | 0.82 | 26 | empty |
| 2 | 220 | 0.63 | 0.82 | 29 | empty |
| 3 | 233 | 0.62 | 0.81 | 34 | empty |
| 4 | 264 | 0.60 | 0.80 | 32 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1004 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 983 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 755 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 752 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 130 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WKK · Identification of the glycan target of the nematotoxic fungal galectin CGL2 in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9P4R8 · AlphaFold monomer V2.0 prediction for galectin-2 (Q9P4R8) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q9P4R8
- Elsewhere: RCSB PDB 2WKK · PDBe 2WKK · UniProt Q9P4R8
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