MolNFT v1 · #151035 · protein
Echovirus 18 native particle
6HBG · Echovirus 18 viral protein 1: “Echovirus 18 native particle”. Electron microscopy, 2 ligands (PLM, GUN), 10 pockets (best druggability 0.76). MolNFT v1 #151035 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HBG
- Type
- protein
- Length
- 784 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Echovirus 18 viral protein 1; Echovirus 18 viral protein 2; Echovirus 18 viral protein 3…
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- Q8V635
- Ligands
- PLM, GUN
- Pockets
- 10 · best druggability 0.76
Structure
electron microscopy · 4 distinct chains · 7% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Echovirus 18 viral protein 1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 261 | 7% helix, 30% strand | Q8V635 |
| B | Echovirus 18 viral protein 2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 247 | 10% helix, 36% strand | Q8V635 |
| C | Echovirus 18 viral protein 3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 238 | 4% helix, 31% strand | Q8V635 |
| D | Echovirus 18 viral protein 4 | protein | 38 | 11% helix, 3% strand | Q8V635 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.76 | 0.87 | 59 | PLM |
| 2 | 104 | 0.45 | 0.79 | 21 | empty |
| 3 | 97 | 0.43 | 0.78 | 18 | empty |
| 4 | 67 | 0.43 | 0.81 | 17 | empty |
| 5 | 77 | 0.43 | 0.80 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4146 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 1978 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1553 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1066 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 922 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6HBG · Echovirus 18 native 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 Q8V635
- Elsewhere: RCSB PDB 6HBG · PDBe 6HBG · UniProt Q8V635
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