Research workbench
Structure of coxsackievirus A10
Analyse Structure of coxsackievirus A10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SMG
- 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
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- Q6JKR9
- Ligands
- SPH
- Pockets
- 13 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 11% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 296 | 10% helix, 28% strand | Q6JKR9 |
| B | Capsid protein VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 246 | 10% helix, 38% strand | Q6JKR9 |
| C | Capsid protein VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 240 | 11% helix, 31% strand | Q6JKR9 |
| D | Capsid protein VP4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 41 | 15% helix, 5% strand | Q6JKR9 |
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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.82 | 0.92 | 45 | SPH |
| 2 | 246 | 0.58 | 0.79 | 34 | empty |
| 3 | 182 | 0.52 | 0.78 | 30 | empty |
| 4 | 297 | 0.52 | 0.74 | 44 | empty |
| 5 | 142 | 0.45 | 0.77 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3966 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2481 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1745 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1183 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 882 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6SMG · Structure of Coxsackievirus A10 · 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 Q6JKR9
- Elsewhere: RCSB PDB 6SMG · PDBe 6SMG · UniProt Q6JKR9
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