Research workbench
Peanut lectin-lactose complex crystallized in orthorhombic form at acidic pH
Analyse Peanut lectin-lactose complex crystallized in orthorhombic form at acidic pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V6J
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-binding lectin
- UniProt
- P02872
- Ligands
- GLC, GAL, CA, MN
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Galactose-binding lectin | protein | 232 | 4% helix, 50% strand | P02872 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.77 | 0.81 | 96 | empty |
| 2 | 147 | 0.44 | 0.76 | 24 | empty |
| 3 | 147 | 0.44 | 0.76 | 30 | empty |
| 4 | 87 | 0.37 | 0.76 | 20 | empty |
| 5 | 103 | 0.37 | 0.75 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–D · 952 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 944 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 594 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 58 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1V6J · peanut lectin-lactose complex crystallized in orthorhombic form at acidic pH · the same entry in another collection · chain A against A, TM-score 1.00
- P02872 · AlphaFold monomer V2.0 prediction for galactose-binding lectin (P02872) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P02872
- Elsewhere: RCSB PDB 1V6J · PDBe 1V6J · UniProt P02872
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