Research workbench
Structure and genome release mechanism of human cardiovirus saffold virus-3
Analyse Structure and genome release mechanism of human cardiovirus saffold virus-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A8F
- Type
- protein
- Length
- 666 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human saffold virus-3 VP1; Genome polyphuman saffold virus-3 VP3 protein; Human saffold…
- UniProt
- C0MHL9, E3TMG9
- Pockets
- 10 · best druggability 0.70
Structure
electron microscopy · 3 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human saffold virus-3 VP1 | protein | 219 | 4% helix, 37% strand | C0MHL9 |
| B | Genome polyphuman saffold virus-3 VP3 protein | protein | 189 | 9% helix, 39% strand | E3TMG9 |
| C | Human saffold virus-3 VP2 | protein | 258 | 12% helix, 37% strand | C0MHL9 |
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.70 | 0.90 | 24 | empty |
| 2 | 169 | 0.50 | 0.77 | 22 | empty |
| 3 | 190 | 0.50 | 0.76 | 31 | empty |
| 4 | 129 | 0.42 | 0.75 | 20 | empty |
| 5 | 93 | 0.40 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1844 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1245 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 910 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5A8F · Structure and genome release mechanism of human cardiovirus Saffold virus-3 · 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 C0MHL9
- Every structure of UniProt E3TMG9
- Elsewhere: RCSB PDB 5A8F · PDBe 5A8F · UniProt C0MHL9 · UniProt E3TMG9
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