MolNFT v1 · #177191 · protein
ECHOVIRUS3 empty compacted particle
7EAI · Capsid protein VP1: “ECHOVIRUS3 empty compacted particle”. Electron microscopy, 1 ligand (SPH), 8 pockets (best druggability 0.77). MolNFT v1 #177191 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EAI
- Type
- protein
- Length
- 758 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP0; Capsid protein VP3
- UniProt
- A0A6M4MJE3
- Ligands
- SPH
- Pockets
- 8 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 8% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 235 | 8% helix, 28% strand | A0A6M4MJE3 |
| B | Capsid protein VP0 | protein | 285 | 7% helix, 20% strand | A0A6M4MJE3 |
| C | Capsid protein VP3 | protein | 238 | 11% helix, 26% strand | A0A6M4MJE3 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.77 | 0.86 | 73 | SPH |
| 2 | 248 | 0.50 | 0.74 | 33 | empty |
| 3 | 81 | 0.49 | 0.83 | 21 | empty |
| 4 | 80 | 0.43 | 0.80 | 19 | empty |
| 5 | 173 | 0.42 | 0.73 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3576 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2211 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1973 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7EAI · Echovirus3 empty compacted 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 A0A6M4MJE3
- Elsewhere: RCSB PDB 7EAI · PDBe 7EAI · UniProt A0A6M4MJE3
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