MolNFT v1 · #52069 · protein
Capsid structure of sesbania mosaic virus coat protein deletion mutant RCP(DELTA 48 to 59)
2VQ0: “Capsid structure of sesbania mosaic virus coat protein deletion mutant RCP(DELTA 48 to 59)”. X-ray diffraction, 1 ligand (CA), 1 pocket (best druggability 0.39). MolNFT v1 #52069 on GenesisL1: 3D structure, binding sites and pockets…
- 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
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