MolNFT v1 · #152553 · protein
Cryo-EM structure of full echovirus 6 particle at pH 7.4
6ILP · Capsid protein VP1: “Cryo-EM structure of full echovirus 6 particle at pH 7.4”. Electron microscopy, 1 ligand (SPH), 12 pockets (best druggability 0.79). MolNFT v1 #152553 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6ILP
- Type
- protein
- Length
- 823 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- Ligands
- SPH
- Pockets
- 12 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 8% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 275 | 9% helix, 30% strand | — |
| B | Capsid protein VP2 | protein | 252 | 8% helix, 35% strand | — |
| C | Capsid protein VP3 | protein | 238 | 8% helix, 29% strand | — |
| D | Capsid protein VP4 | protein | 58 | 5% helix, 14% strand | — |
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 | 593 | 0.79 | 0.85 | 87 | SPH |
| 2 | 90 | 0.50 | 0.82 | 18 | empty |
| 3 | 114 | 0.46 | 0.79 | 21 | empty |
| 4 | 87 | 0.44 | 0.80 | 24 | empty |
| 5 | 209 | 0.44 | 0.73 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4252 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2140 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1610 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1201 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 952 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6ILP · Cryo-EM structure of full Echovirus 6 particle at PH 7.4 · 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
- Elsewhere: RCSB PDB 6ILP · PDBe 6ILP
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