Research workbench
Crystal structure echovirus 7
Analyse Crystal structure echovirus 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X5I
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- Q6W9E5
- Ligands
- DAO
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 277 | 9% helix, 32% strand | Q6W9E5 |
| B | VP2 | protein | 252 | 11% helix, 35% strand | Q6W9E5 |
| C | VP3 | protein | 238 | 9% helix, 28% strand | Q6W9E5 |
| D | VP4 | protein | 61 | 11% helix, 15% strand | Q6W9E5 |
Ligands and binding sites
- DAO · Lauric acid · ligand · chains A
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 | 179 | 0.81 | 0.95 | 35 | DAO |
| 2 | 212 | 0.53 | 0.77 | 35 | empty |
| 3 | 104 | 0.53 | 0.84 | 25 | empty |
| 4 | 68 | 0.52 | 0.86 | 19 | empty |
| 5 | 134 | 0.45 | 0.77 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4382 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 2069 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1615 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1176 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 895 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2X5I · Crystal structure echovirus 7 · 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 Q6W9E5
- Elsewhere: RCSB PDB 2X5I · PDBe 2X5I · UniProt Q6W9E5
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