Research workbench
Structure of the rhombohedral crystal of canavalin from jack bean
Analyse Structure of the rhombohedral crystal of canavalin from jack bean in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DGW
- Type
- protein
- Length
- 346 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Canavalin
- UniProt
- P50477
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Canavalin | protein | 178 | 17% helix, 44% strand | P50477 |
| X | Canavalin | protein | 76 | 5% helix, 54% strand | P50477 |
| Y | Canavalin | protein | 92 | 14% helix, 34% strand | P50477 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.26 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- X–Y · 3588 Ų buried · 87 hydrogen bonds · protein-protein
- A–X · 930 Ų buried · 10 hydrogen bonds · protein-protein
- A–Y · 746 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 P50477
- Elsewhere: RCSB PDB 1DGW · PDBe 1DGW · UniProt P50477
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