Research workbench
Capsid structure of sesbania mosaic virus coat protein deletion mutant RCP(DELTA 48 to 59)
Analyse Capsid structure of sesbania mosaic virus coat protein deletion mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VQ0
- Type
- protein
- Length
- 606 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein
- UniProt
- Q9EB06
- Ligands
- CA
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coat protein | protein | 196 | 22% helix, 39% strand | Q9EB06 |
| B | Coat protein | protein | 197 | 21% helix, 40% strand | Q9EB06 |
| C | Coat protein | protein | 213 | 18% helix, 39% strand | Q9EB06 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, C, B
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 | 108 | 0.39 | 0.75 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 994 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 988 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 978 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2VQ0 · Capsid structure of Sesbania mosaic virus coat protein deletion mutant rCP(delta 48 to 59) · 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
- Every structure of UniProt Q9EB06
- Elsewhere: RCSB PDB 2VQ0 · PDBe 2VQ0 · UniProt Q9EB06
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.