Research workbench
Dolichos biflorus seed lectin in complex with the blood group a trisaccharide
Analyse Dolichos biflorus seed lectin in complex with the blood group a trisaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LU2
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- UniProt
- P05045
- Ligands
- A2G, CA, MN
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lectin | protein | 253 | 8% helix, 45% strand | P05045 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.64 | 0.79 | 26 | empty |
| 2 | 68 | 0.31 | 0.75 | 22 | empty |
| 3 | 60 | 0.31 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 926 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1LU2 · Dolichos biflorus seed lectin in complex with the blood group a trisaccharide · the same entry in another collection · chain A against A, TM-score 1.00
- P05045 · AlphaFold monomer V2.0 prediction for seed lectin subunit I (P05045) · 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 P05045
- Elsewhere: RCSB PDB 1LU2 · PDBe 1LU2 · UniProt P05045
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