Research workbench
Crystal structure of basic winged bean lectin in complex with 2ME-O-D- galactose
Analyse Crystal structure of basic winged bean lectin in complex with 2ME-O-D- galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DTW
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic agglutinin
- UniProt
- O24313
- Ligands
- 2GS, NAG, FUC, NDG, BMA, FUL, CA, MN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Basic agglutinin | protein | 237 | 4% helix, 45% strand | O24313 |
Ligands and binding sites
- 2GS · 2-O-methyl-alpha-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 5 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar
- BMA · beta-D-mannopyranose · sugar
- FUL · beta-L-fucopyranose · sugar
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.76 | 0.80 | 81 | empty |
| 2 | 59 | 0.37 | 0.80 | 16 | empty |
| 3 | 84 | 0.36 | 0.76 | 19 | empty |
| 4 | 64 | 0.33 | 0.76 | 18 | 2GS |
| 5 | 77 | 0.33 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 836 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 822 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 306 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 288 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan (N-glycosylation).
Compared structures
- 2DTW · Crystal Structure of basic winged bean lectin in complex with 2Me-O-D-Galactose · the same entry in another collection · chain A against A, TM-score 1.00
- O24313 · AlphaFold monomer V2.0 prediction for basic agglutinin (O24313) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O24313
- Elsewhere: RCSB PDB 2DTW · PDBe 2DTW · UniProt O24313
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