Research workbench
Binding of Benzoic Acid and Anions Within the Cupin Domains of the Vicillin Protein Canavalin from Jack Bean (canavalia ensiformis): Crystal Structures
Analyse Binding of Benzoic Acid and Anions Within the Cupin Domains of the Vicillin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V7G
- Type
- protein
- Length
- 357 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Canavalia ensiformis
- Molecule
- Canavalin
- UniProt
- P50477
- Ligands
- BEZ
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.4 · 1 distinct chain · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Canavalin | protein | 357 | 16% helix, 42% strand | P50477 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains A
- ACT · Acetate ion · additive · chains A
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.74 | 0.99 | 15 | BEZ |
| 2 | 58 | 0.27 | 0.73 | 17 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6V7G · Binding of benzoic acid and anions within the cupin domains of the vicillin protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P50477 · AlphaFold monomer V2.0 prediction for canavalin (P50477) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 6V7G · PDBe 6V7G · UniProt P50477
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