Research workbench
Three-dimensional structures of complexes of lathyrus ochrus isolectin I with glucose and mannose: fine specificity of the monosaccharide- binding site
Analyse Three-dimensional structures of complexes of lathyrus ochrus isolectin I with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LOA
- Type
- protein
- Length
- 908 residues
- Chains
- 8
- 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
- GYP, CA, MN
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Legume isolectin I (alpha chain) | protein | 180 | 3% helix, 45% strand | P04122 |
| B, F | Legume isolectin I (beta chain) | protein | 47 | 9% helix, 64% strand | P12306 |
| D, H | Legume isolectin I (beta chain) | protein | 47 | 9% helix, 62% strand | P12306 |
Ligands and binding sites
- GYP · methyl alpha-D-glucopyranoside · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 4 copies · chains A, C, E, G
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.72 | 0.77 | 84 | empty |
| 2 | 92 | 0.50 | 0.83 | 20 | empty |
| 3 | 71 | 0.46 | 0.83 | 19 | empty |
| 4 | 94 | 0.41 | 0.78 | 19 | empty |
| 5 | 64 | 0.32 | 0.76 | 15 | empty |
Interfaces
14 interfaces between chains.
- C–D · 3915 Ų buried · 91 hydrogen bonds · protein-protein
- A–B · 3900 Ų buried · 89 hydrogen bonds · protein-protein
- E–F · 3887 Ų buried · 92 hydrogen bonds · protein-protein
- G–H · 3884 Ų buried · 94 hydrogen bonds · protein-protein
- E–G · 850 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1LOA · Three-dimensional structures of complexes of lathyrus ochrus isolectin I with glucose and… · the same entry in another collection · chain G against G, 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
- P12306 · AlphaFold monomer V2.0 prediction for MANNOSE/GLUCOSE-specific lectin alpha 1 chain… · a predicted model of the same protein · chain D against A, TM-score 0.96
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 1LOA · PDBe 1LOA · UniProt P04122 · UniProt P12306
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