MolNFT v1 · #142950 · protein
Cryo-EM structure of CVA10 mature virus
6AKS · VP1: “Cryo-EM structure of CVA10 mature virus”. Electron microscopy, 1 ligand (SPH), 11 pockets (best druggability 0.80). MolNFT v1 #142950 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AKS
- Type
- protein
- Length
- 824 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- W0G0K3, A0A0C5AZ80, A0A0C5AWF6, Q75Q92
- Ligands
- SPH
- Pockets
- 11 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 10% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 287 | 11% helix, 29% strand | W0G0K3 |
| B | VP2 | protein | 246 | 11% helix, 35% strand | A0A0C5AZ80 |
| C | VP3 | protein | 240 | 8% helix, 31% strand | A0A0C5AWF6 |
| D | VP4 | protein | 51 | 8% helix, 6% strand | Q75Q92 |
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
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.80 | 0.88 | 61 | SPH |
| 2 | 124 | 0.50 | 0.80 | 25 | empty |
| 3 | 89 | 0.46 | 0.80 | 20 | empty |
| 4 | 134 | 0.45 | 0.76 | 24 | empty |
| 5 | 102 | 0.44 | 0.79 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3845 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2378 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1721 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1349 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 895 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6AKS · Cryo-EM structure of CVA10 mature virus · 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 W0G0K3
- Every structure of UniProt A0A0C5AZ80
- Every structure of UniProt A0A0C5AWF6
- Every structure of UniProt Q75Q92
- Elsewhere: RCSB PDB 6AKS · PDBe 6AKS · UniProt W0G0K3 · UniProt A0A0C5AZ80 · UniProt A0A0C5AWF6 · UniProt Q75Q92
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