MolNFT v1 · #108920 · protein
Crystal structure of human enterovirus D68
4WM8 · VP1: “Crystal structure of human enterovirus D68”. X-ray diffraction, 1 ligand (DKA), 12 pockets (best druggability 0.79). MolNFT v1 #108920 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WM8
- Type
- protein
- Length
- 805 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- Q9YLJ3, Q68T42, Q8QWD4
- Ligands
- DKA
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 281 | 10% helix, 35% strand | Q9YLJ3 |
| B | VP2 | protein | 238 | 13% helix, 37% strand | Q68T42 |
| C | VP3 | protein | 247 | 9% helix, 30% strand | Q68T42 |
| D | VP4 | protein | 39 | 18% helix, 8% strand | Q8QWD4 |
Ligands and binding sites
- DKA · Decanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.79 | 0.86 | 55 | DKA |
| 2 | 58 | 0.72 | 0.98 | 22 | empty |
| 3 | 227 | 0.53 | 0.77 | 32 | empty |
| 4 | 169 | 0.50 | 0.78 | 28 | empty |
| 5 | 106 | 0.43 | 0.78 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4718 Ų buried · 86 hydrogen bonds · protein-protein
- A–B · 2116 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1849 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1203 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 943 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4WM8 · Crystal Structure of Human Enterovirus D68 · 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 Q9YLJ3
- Every structure of UniProt Q68T42
- Every structure of UniProt Q8QWD4
- Elsewhere: RCSB PDB 4WM8 · PDBe 4WM8 · UniProt Q9YLJ3 · UniProt Q68T42 · UniProt Q8QWD4
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