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Crystal structure of coxsackievirus A24V soaked with disialyllacto-N- tetraose (dslnt)
Analyse Crystal structure of coxsackievirus A24V soaked with disialyllacto-N- tetraose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q4Y
- Type
- protein
- Length
- 836 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coxsackievirus capsid protein VP1; Coxsackievirus capsid protein VP2; Coxsackievirus…
- UniProt
- V9VEF3
- Ligands
- MYR, SIA, CA, MG, CL
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Coxsackievirus capsid protein VP1 | protein | 281 | 12% helix, 31% strand | V9VEF3 |
| 2 | Coxsackievirus capsid protein VP2 | protein | 264 | 15% helix, 36% strand | V9VEF3 |
| 3 | Coxsackievirus capsid protein VP3 | protein | 234 | 8% helix, 30% strand | V9VEF3 |
| 4 | Coxsackievirus capsid protein VP4 | protein | 57 | 12% helix, 16% strand | V9VEF3 |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains 4
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains 1
- CA · Calcium ion · metal · 5 copies · chains 1, 4, 2, 3
- MG · Magnesium ion · metal · chains 2
- CL · Chloride ion · ion · 7 copies · chains 1, 3, 2, 4
- HEZ · Hexane-1,6-diol · additive · 2 copies · chains 1, 2
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.74 | 0.84 | 58 | empty |
| 2 | 125 | 0.59 | 0.85 | 26 | empty |
| 3 | 73 | 0.53 | 0.86 | 19 | empty |
| 4 | 65 | 0.48 | 0.84 | 19 | empty |
| 5 | 185 | 0.46 | 0.75 | 30 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 3956 Ų buried · 75 hydrogen bonds · protein-protein
- 1–2 · 2438 Ų buried · 45 hydrogen bonds · protein-protein
- 2–3 · 1720 Ų buried · 20 hydrogen bonds · protein-protein
- 1–4 · 1032 Ų buried · 13 hydrogen bonds · protein-protein
- 3–4 · 910 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 4Q4Y · Crystal structure of Coxsackievirus A24v soaked with Disialyllacto-N-tetraose (DSLNT) · the same entry in another collection · chain 1 against 1, 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 V9VEF3
- Elsewhere: RCSB PDB 4Q4Y · PDBe 4Q4Y · UniProt V9VEF3
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