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
- 1LGC
- Type
- protein
- Length
- 690 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Legume isolectin II (alpha chain); Dipeptide; Legume isolectin II (beta chain)
- UniProt
- P04122, P12307
- Ligands
- NAG, MAN, FUC, BMA, GAL, SIA, CA, MN
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Legume isolectin II (alpha chain) | protein | 181 | 3% helix, 44% strand | P04122 |
| H, I | Dipeptide | protein | 1 | 0% helix, 0% strand | — |
| B | Legume isolectin II (beta chain) | protein | 50 | 6% helix, 60% strand | P12307 |
| D | Legume isolectin II (beta chain) | protein | 47 | 0% helix, 64% strand | P12307 |
| J | Dipeptide | protein | 2 | 0% helix, 0% strand | — |
| F | Legume isolectin II (beta chain) | protein | 46 | 9% helix, 59% strand | P12307 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, H, B, C, I, D, E, J, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, C, D, E, F
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains C, E
- CA · Calcium ion · metal · 3 copies · chains A, C, E
- MN · Manganese (II) ion · metal · 3 copies · chains A, C, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C, E
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 | 489 | 0.64 | 0.77 | 55 | MPD |
| 2 | 79 | 0.37 | 0.77 | 14 | empty |
| 3 | 62 | 0.32 | 0.76 | 16 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3919 Ų buried · 101 hydrogen bonds · protein-protein
- C–D · 3862 Ų buried · 97 hydrogen bonds · protein-protein
- E–F · 3849 Ų buried · 95 hydrogen bonds · protein-protein
- A–C · 759 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 237 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 1LGC · Interaction of a legume lectin with the N2 fragment of human lactotransferrin or with the… · the same entry in another collection · chain F against F, 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
- P12307 · AlphaFold monomer V2.0 prediction for MANNOSE/GLUCOSE-specific lectin alpha 2 chain… · a predicted model of the same protein · chain F against A, TM-score 0.95
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
- Elsewhere: RCSB PDB 1LGC · PDBe 1LGC · UniProt P04122 · UniProt P12307
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