MolNFT v1 · #162795 · protein
Echovirus 1 intact particle
6RJF · VP1: “Echovirus 1 intact particle”. Electron microscopy, 1 ligand (PLM), 16 pockets (best druggability 0.79). MolNFT v1 #162795 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RJF
- Type
- protein
- Length
- 836 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- O91734
- Ligands
- PLM
- Pockets
- 16 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | VP1 | protein | 281 | 9% helix, 32% strand | O91734 |
| 2 | VP2 | protein | 255 | 12% helix, 39% strand | O91734 |
| 3 | VP3 | protein | 239 | 10% helix, 33% strand | O91734 |
| 4 | VP4 | protein | 61 | 11% helix, 15% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains 1
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.79 | 0.86 | 60 | PLM |
| 2 | 86 | 0.55 | 0.85 | 21 | empty |
| 3 | 85 | 0.53 | 0.85 | 15 | empty |
| 4 | 146 | 0.51 | 0.79 | 22 | empty |
| 5 | 146 | 0.49 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 4286 Ų buried · 65 hydrogen bonds · protein-protein
- 1–2 · 2086 Ų buried · 31 hydrogen bonds · protein-protein
- 2–3 · 1622 Ų buried · 16 hydrogen bonds · protein-protein
- 1–4 · 1550 Ų buried · 20 hydrogen bonds · protein-protein
- 3–4 · 937 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6RJF · Echovirus 1 intact particle · the same entry in another collection · chain 3 against 3, 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 O91734
- Elsewhere: RCSB PDB 6RJF · PDBe 6RJF · UniProt O91734
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.