Research workbench
Denguev-2 capsid structure
Analyse Denguev-2 capsid structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VSO
- Type
- protein
- Length
- 464 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid premembrane protein
- UniProt
- A0A2D2BF61
- Ligands
- NO3
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid premembrane protein | protein | 77 | 79% helix, 1% strand | A0A2D2BF61 |
| B | Capsid premembrane protein | protein | 78 | 74% helix, 3% strand | A0A2D2BF61 |
| C, E | Capsid premembrane protein | protein | 76 | 79% helix, 0% strand | A0A2D2BF61 |
| D | Capsid premembrane protein | protein | 78 | 74% helix, 1% strand | A0A2D2BF61 |
| F | Capsid premembrane protein | protein | 79 | 66% helix, 0% strand | A0A2D2BF61 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 20 copies · chains A, B, D, C, E, F
- GOL · Glycerol · additive · 3 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.75 | 0.80 | 53 | empty |
| 2 | 210 | 0.70 | 0.86 | 33 | NO3 |
| 3 | 177 | 0.47 | 0.76 | 30 | empty |
| 4 | 55 | 0.32 | 0.76 | 13 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2303 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2215 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 2189 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 425 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 187 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VSO · DengueV-2 Capsid Structure · 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 A0A2D2BF61
- Elsewhere: RCSB PDB 6VSO · PDBe 6VSO · UniProt A0A2D2BF61
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