Research workbench
Crystal structure of the vicilin from solanum melongena revealed existence of different anionic ligands in structurally similar pockets
Analyse Crystal structure of the vicilin from solanum melongena revealed existence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CAD
- Type
- protein
- Length
- 379 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SM80.1 vicilin
- Ligands
- PCA, MG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SM80.1 vicilin | protein | 379 | 18% helix, 39% strand | — |
Ligands and binding sites
- PCA · Pyroglutamic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.77 | 0.99 | 27 | PCA |
| 2 | 79 | 0.52 | 0.84 | 18 | empty |
| 3 | 98 | 0.48 | 0.81 | 21 | empty |
Compared structures
- 5CAD · Crystal structure of the vicilin from Solanum melongena revealed existence of different… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5CAD · PDBe 5CAD
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.