MolNFT v1 · #142705 · protein
The structure of CVA10 virus mature virion
6ACU · VP1: “The structure of CVA10 virus mature virion”. Electron microscopy, 1 ligand (SPH), 12 pockets (best druggability 0.85). MolNFT v1 #142705 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ACU
- Type
- protein
- Length
- 808 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- A0A1V0FT21, Q75Q92
- Ligands
- SPH
- Pockets
- 12 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 284 | 7% helix, 29% strand | A0A1V0FT21 |
| B | VP2 | protein | 243 | 8% helix, 39% strand | A0A1V0FT21 |
| C | VP3 | protein | 240 | 10% helix, 32% strand | A0A1V0FT21 |
| D | VP4 | protein | 41 | 15% helix, 7% strand | Q75Q92 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.85 | 0.93 | 65 | SPH |
| 2 | 53 | 0.58 | 0.91 | 21 | empty |
| 3 | 143 | 0.48 | 0.79 | 30 | empty |
| 4 | 141 | 0.47 | 0.78 | 23 | empty |
| 5 | 134 | 0.47 | 0.78 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3824 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2383 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1784 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1381 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 862 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6ACU · The structure of CVA10 virus mature virion · 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 A0A1V0FT21
- Every structure of UniProt Q75Q92
- Elsewhere: RCSB PDB 6ACU · PDBe 6ACU · UniProt A0A1V0FT21 · UniProt Q75Q92
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