Research workbench
Murine polyomavirus hexavalent capsomer, subparticle reconstruction
Analyse Murine polyomavirus hexavalent capsomer, subparticle reconstruction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K25
- Type
- protein
- Length
- 1,796 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- A0A247D727
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 5 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 366 | 6% helix, 31% strand | A0A247D727 |
| B | Capsid protein VP1 | protein | 367 | 8% helix, 32% strand | A0A247D727 |
| C | Capsid protein VP1 | protein | 357 | 9% helix, 31% strand | A0A247D727 |
| D | Capsid protein VP1 | protein | 340 | 10% helix, 32% strand | A0A247D727 |
| E | Capsid protein VP1 | protein | 366 | 8% helix, 31% strand | A0A247D727 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.74 | 0.96 | 28 | empty |
| 2 | 112 | 0.74 | 0.95 | 26 | empty |
| 3 | 806 | 0.73 | 0.78 | 77 | empty |
| 4 | 735 | 0.72 | 0.78 | 77 | empty |
| 5 | 723 | 0.72 | 0.78 | 75 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3179 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2816 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 2809 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 2719 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2713 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7K25 · Murine polyomavirus hexavalent capsomer, subparticle reconstruction · 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 A0A247D727
- Elsewhere: RCSB PDB 7K25 · PDBe 7K25 · UniProt A0A247D727
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