Research workbench
Crystal structure of basic winged bean lectin in complex with methyl- alpha-N-acetyl-D galactosamine
Analyse Crystal structure of basic winged bean lectin in complex with methyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DU1
- 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
- MGC, NAG, FUC, CA, MN
- Pockets
- 7 · best druggability 0.74
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
- MGC · methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies
- 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 | 684 | 0.74 | 0.80 | 74 | empty |
| 2 | 61 | 0.39 | 0.80 | 15 | empty |
| 3 | 65 | 0.34 | 0.77 | 17 | MGC |
| 4 | 60 | 0.32 | 0.76 | 17 | empty |
| 5 | 65 | 0.31 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 832 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 832 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 301 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 292 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan (N-glycosylation).
Compared structures
- 2DU1 · Crystal Structure of basic winged bean lectin in complex with Methyl-alpha-N-acetyl-D… · 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 2DU1 · PDBe 2DU1 · UniProt O24313
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