MolNFT v1 · #152466 · protein
Cryo-EM structure of cv-A10 mature virion
6IIJ · VP1: “Cryo-EM structure of cv-A10 mature virion”. Electron microscopy, 1 ligand (SPH), 13 pockets (best druggability 0.82). MolNFT v1 #152466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IIJ
- Type
- protein
- Length
- 814 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- A0A1B3Z4Y8
- Ligands
- SPH
- Pockets
- 13 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 12% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 287 | 10% helix, 29% strand | A0A1B3Z4Y8 |
| B | VP2 | protein | 246 | 13% helix, 36% strand | A0A1B3Z4Y8 |
| C | VP3 | protein | 240 | 12% helix, 33% strand | A0A1B3Z4Y8 |
| D | VP4 | protein | 41 | 17% helix, 5% strand | A0A1B3Z4Y8 |
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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.82 | 0.91 | 56 | SPH |
| 2 | 54 | 0.70 | 0.97 | 19 | empty |
| 3 | 236 | 0.54 | 0.77 | 33 | empty |
| 4 | 80 | 0.53 | 0.85 | 22 | empty |
| 5 | 160 | 0.52 | 0.79 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3816 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2279 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1704 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1306 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 848 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6IIJ · Cryo-EM structure of CV-A10 mature virion · 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 A0A1B3Z4Y8
- Elsewhere: RCSB PDB 6IIJ · PDBe 6IIJ · UniProt A0A1B3Z4Y8
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