Research workbench
Cryoem structure of merkel cell polyomavirus virus-like particle
Analyse Cryoem structure of merkel cell polyomavirus virus-like particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZML
- Type
- protein
- Length
- 2,158 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- B0G0W3
- Pockets
- 16 · best druggability 0.73
Structure
electron microscopy · 6 distinct chains · 7% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 359 | 5% helix, 26% strand | B0G0W3 |
| B | Capsid protein VP1 | protein | 368 | 8% helix, 29% strand | B0G0W3 |
| C | Capsid protein VP1 | protein | 362 | 9% helix, 21% strand | B0G0W3 |
| D | Capsid protein VP1 | protein | 351 | 9% helix, 25% strand | B0G0W3 |
| E | Capsid protein VP1 | protein | 361 | 8% helix, 25% strand | B0G0W3 |
| F | Capsid protein VP1 | protein | 357 | 4% helix, 27% strand | B0G0W3 |
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.73 | 0.77 | 93 | empty |
| 2 | 361 | 0.72 | 0.84 | 43 | empty |
| 3 | 1071 | 0.71 | 0.75 | 96 | empty |
| 4 | 834 | 0.70 | 0.76 | 79 | empty |
| 5 | 756 | 0.70 | 0.76 | 70 | empty |
Interfaces
7 interfaces between chains.
- B–C · 3114 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2756 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 2669 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2608 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2607 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6ZML · CryoEM Structure of Merkel Cell Polyomavirus Virus-like Particle · 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 B0G0W3
- Elsewhere: RCSB PDB 6ZML · PDBe 6ZML · UniProt B0G0W3
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