MolNFT v1 · #174892 · protein
Echovirus 30 F-particle
7C9S · VP1: “Echovirus 30 F-particle”. Electron microscopy, 2 ligands (MYR, SPH), 12 pockets (best druggability 0.78). MolNFT v1 #174892 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7C9S
- Type
- protein
- Length
- 822 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- Q33C85
- Ligands
- MYR, SPH
- Pockets
- 12 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 276 | 10% helix, 31% strand | — |
| B | VP2 | protein | 251 | 9% helix, 38% strand | — |
| C | VP3 | protein | 238 | 7% helix, 32% strand | — |
| D | VP4 | protein | 57 | 11% helix, 16% strand | Q33C85 |
Ligands and binding sites
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 | 534 | 0.78 | 0.84 | 74 | SPH |
| 2 | 122 | 0.51 | 0.81 | 38 | empty |
| 3 | 130 | 0.47 | 0.78 | 22 | empty |
| 4 | 130 | 0.47 | 0.78 | 27 | empty |
| 5 | 82 | 0.41 | 0.79 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4296 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 2105 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1667 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1249 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 930 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 lipid (covalent ligand, myristoylation).
Compared structures
- 7C9S · Echovirus 30 F-particle · 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 Q33C85
- Elsewhere: RCSB PDB 7C9S · PDBe 7C9S · UniProt Q33C85
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