Research workbench
X-ray structure of a biantennary octasaccharide-lectin complex at 2.3 ångströms resolution
Analyse X-ray structure of a biantennary octasaccharide-lectin complex at 2.3 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LOF
- Type
- protein
- Length
- 460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Legume isolectin I (alpha chain); Legume isolectin I (beta chain)
- UniProt
- P04122, P12306
- Ligands
- NAG, MAN, GAL, BMA, CA, MN
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Legume isolectin I (alpha chain) | protein | 181 | 2% helix, 44% strand | P04122 |
| B | Legume isolectin I (beta chain) | protein | 47 | 6% helix, 62% strand | P12306 |
| C | Legume isolectin I (alpha chain) | protein | 180 | 2% helix, 45% strand | P04122 |
| D | Legume isolectin I (beta chain) | protein | 52 | 6% helix, 58% strand | P12306 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.47 | 0.79 | 22 | empty |
| 2 | 104 | 0.37 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4052 Ų buried · 103 hydrogen bonds · protein-protein
- A–B · 3973 Ų buried · 97 hydrogen bonds · protein-protein
- A–C · 780 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 164 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 134 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1LOF · X-ray structure of a biantennary octasaccharide-lectin complex at 2.3 ångströms resolution · the same entry in another collection · chain D against D, 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 C against A, TM-score 1.00
- P12306 · AlphaFold monomer V2.0 prediction for MANNOSE/GLUCOSE-specific lectin alpha 1 chain… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P12306
- Elsewhere: RCSB PDB 1LOF · PDBe 1LOF · UniProt P04122 · UniProt P12306
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