Research workbench
Interaction of a legume lectin with the N2 fragment of human lactotransferrin or with the isolated biantennary glycopeptide: role of the fucose moiety
Analyse Interaction of a legume lectin with the N2 fragment of human lactotransferrin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LGB
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Legume isolectin II (alpha chain); Legume isolectin II (beta chain); Lactotransferrin (N2…
- UniProt
- P04122, P12307, P02788
- Ligands
- NAG, MAN, BMA, GAL, FUC, MN, CA
- Pockets
- 1 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Legume isolectin II (alpha chain) | protein | 181 | 3% helix, 41% strand | P04122 |
| B | Legume isolectin II (beta chain) | protein | 46 | 9% helix, 61% strand | P12307 |
| C | Lactotransferrin (N2 fragment) | protein | 159 | 30% helix, 9% strand | P02788 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains A, B
- GAL · beta-D-galactopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- MN · Manganese (II) ion · metal · chains A
- CA · Calcium 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 | 128 | 0.41 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3840 Ų buried · 102 hydrogen bonds · protein-protein
- A–C · 185 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1LGB · Interaction of a legume lectin with the N2 fragment of human lactotransferrin or with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P04122 · AlphaFold monomer V2.0 prediction for lectin beta-1 and beta-2 chains (P04122) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P02788 · AlphaFold monomer V2.0 prediction for lactotransferrin (P02788) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P12307 · AlphaFold monomer V2.0 prediction for MANNOSE/GLUCOSE-specific lectin alpha 2 chain… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P04122
- Every structure of UniProt P12307
- Every structure of UniProt P02788
- Elsewhere: RCSB PDB 1LGB · PDBe 1LGB · UniProt P04122 · UniProt P12307 · UniProt P02788
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