MolNFT v1 · #171952 · protein
Crystal structure of merkel cell polyomavirus virus-like particle
6ZLZ · Capsid protein VP1: “Crystal structure of merkel cell polyomavirus virus-like particle”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.75). MolNFT v1 #171952 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6ZLZ
- Type
- protein
- Length
- 2,156 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- B0G0W3
- Ligands
- CA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 359 | 9% helix, 31% strand | B0G0W3 |
| B | Capsid protein VP1 | protein | 371 | 11% helix, 31% strand | B0G0W3 |
| C | Capsid protein VP1 | protein | 360 | 12% helix, 28% strand | B0G0W3 |
| D | Capsid protein VP1 | protein | 346 | 11% helix, 30% strand | B0G0W3 |
| E | Capsid protein VP1 | protein | 362 | 12% helix, 29% strand | B0G0W3 |
| F | Capsid protein VP1 | protein | 358 | 8% helix, 27% strand | B0G0W3 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, C, B, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.75 | 0.77 | 98 | empty |
| 2 | 374 | 0.73 | 0.84 | 44 | empty |
| 3 | 754 | 0.69 | 0.76 | 73 | empty |
| 4 | 699 | 0.67 | 0.76 | 67 | empty |
| 5 | 647 | 0.67 | 0.76 | 78 | empty |
Interfaces
7 interfaces between chains.
- B–C · 3000 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2705 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 2693 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 2670 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2567 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6ZLZ · Crystal 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 6ZLZ · PDBe 6ZLZ · UniProt B0G0W3
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