Research workbench
The 3.5 a resolution structure of the sputnik virophage by cryo-EM
Analyse The 3.5 a resolution structure of the sputnik virophage by cryo-EM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J26
- Type
- protein
- Length
- 6,966 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein V20; Minor virion protein
- UniProt
- B4YNG0, I0CES9
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 7% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M | Capsid protein V20 | protein | 508 | 7% helix, 31% strand | B4YNG0 |
| N | Minor virion protein | protein | 362 | 8% helix, 24% strand | I0CES9 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.87 | 0.89 | 124 | empty |
| 2 | 988 | 0.84 | 0.85 | 116 | empty |
| 3 | 528 | 0.83 | 0.89 | 70 | empty |
| 4 | 804 | 0.82 | 0.85 | 99 | empty |
| 5 | 538 | 0.82 | 0.88 | 58 | empty |
Interfaces
27 interfaces between chains.
- I–J · 4443 Ų buried · 36 hydrogen bonds · protein-protein
- H–J · 4308 Ų buried · 32 hydrogen bonds · protein-protein
- L–M · 4306 Ų buried · 24 hydrogen bonds · protein-protein
- H–I · 4292 Ų buried · 32 hydrogen bonds · protein-protein
- K–M · 4290 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3J26 · The 3.5 A resolution structure of the Sputnik virophage by cryo-EM · 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 B4YNG0
- Every structure of UniProt I0CES9
- Elsewhere: RCSB PDB 3J26 · PDBe 3J26 · UniProt B4YNG0 · UniProt I0CES9
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