Research workbench
Crystal structure of peanut lectin in complex with meso- tetrasulphonatophenylporphyrin and lactose
Analyse Crystal structure of peanut lectin in complex with meso… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RIT
- 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
- SFP, BGC, GAL, CA, MN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Galactose-binding lectin | protein | 232 | 3% helix, 47% strand | P02872 |
Ligands and binding sites
- SFP · 5,10,15,20-tetrakis(4-sulpfonatophenyl)-21H,23H-porphine · ligand · 11 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains C, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.76 | 0.79 | 129 | empty |
| 2 | 148 | 0.48 | 0.77 | 28 | empty |
| 3 | 139 | 0.46 | 0.77 | 22 | empty |
| 4 | 144 | 0.45 | 0.76 | 30 | empty |
| 5 | 91 | 0.36 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–D · 970 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 964 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 696 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 616 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1RIT · Crystal structure of Peanut lectin in complex with meso-tetrasulphonatophenylporphyrin… · 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 0.99
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 1RIT · PDBe 1RIT · UniProt P02872
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