Research workbench
The monosaccharide binding site of lentil lectin: an X-ray and molecular modelling study
Analyse The monosaccharide binding site of lentil lectin: an X-ray and molecular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LEM
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- UniProt
- P02870
- Ligands
- GLC, CA, MN
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin | protein | 181 | 3% helix, 48% strand | P02870 |
| B | Lectin | protein | 47 | 9% helix, 64% strand | P02870 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- CA · Calcium ion · metal · chains A
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.35 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3889 Ų buried · 98 hydrogen bonds · protein-protein
Compared structures
- 1LEM · The monosaccharide binding site of lentil lectin: an X-ray and molecular modelling study · the same entry in another collection · chain A against A, TM-score 1.00
- P02870 · AlphaFold monomer V2.0 prediction for lectin (P02870) · 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 P02870
- Elsewhere: RCSB PDB 1LEM · PDBe 1LEM · UniProt P02870
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