MolNFT v1 · #3837 · protein
The crystal structure of coxsackievirus A9 to 2.9 a resolution
1D4M · Protein (coxsackievirus A9): “The crystal structure of coxsackievirus A9 to 2.9 a resolution”. X-ray diffraction, 2 ligands (W71, MYR), 10 pockets (best druggability 0.78). MolNFT v1 #3837 on GenesisL1: 3D structure, binding sites…
- PDB
- 1D4M
- Type
- protein
- Length
- 835 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (coxsackievirus A9)
- UniProt
- P21404
- Ligands
- W71, MYR
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Protein (coxsackievirus A9) | protein | 284 | 12% helix, 32% strand | P21404 |
| 2 | Protein (coxsackievirus A9) | protein | 252 | 11% helix, 37% strand | P21404 |
| 3 | Protein (coxsackievirus A9) | protein | 238 | 8% helix, 32% strand | P21404 |
| 4 | Protein (coxsackievirus A9) | protein | 61 | 11% helix, 16% strand | P21404 |
Ligands and binding sites
- W71 · 5-(7-(4-(4,5-dihydro-2-oxazolyl)phenoxy)heptyl)-3-methyl isoxazole · ligand · 2 copies · chains 1, 3
- MYR · Myristic acid · ligand · chains 1, 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.78 | 0.85 | 66 | W71 |
| 2 | 58 | 0.51 | 0.86 | 19 | empty |
| 3 | 87 | 0.50 | 0.83 | 22 | empty |
| 4 | 113 | 0.46 | 0.79 | 22 | empty |
| 5 | 188 | 0.45 | 0.74 | 28 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 4305 Ų buried · 76 hydrogen bonds · protein-protein
- 1–2 · 2004 Ų buried · 37 hydrogen bonds · protein-protein
- 2–3 · 1596 Ų buried · 18 hydrogen bonds · protein-protein
- 1–4 · 1431 Ų buried · 25 hydrogen bonds · protein-protein
- 3–4 · 960 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 1D4M · The crystal structure of coxsackievirus A9 to 2.9 a resolution · 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 P21404
- Elsewhere: RCSB PDB 1D4M · PDBe 1D4M · UniProt P21404
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