Research workbench
JC Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules (aromatic linker)
Analyse JC Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZIO
- Type
- protein
- Length
- 1,297 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.751
- Source
- JC polyomavirus
- Molecule
- Major capsid protein VP1
- UniProt
- P03089
- Ligands
- GAL, SIA, BGC, CL
- Pockets
- 14 · best druggability 0.51
Structure
x-ray diffraction · resolution 1.751 · 4 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | Major capsid protein VP1 | protein | 257 | 7% helix, 42% strand | P03089 |
| BBB | Major capsid protein VP1 | protein | 256 | 7% helix, 42% strand | P03089 |
| CCC, DDD | Major capsid protein VP1 | protein | 263 | 7% helix, 41% strand | P03089 |
| EEE | Major capsid protein VP1 | protein | 258 | 7% helix, 42% strand | P03089 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 3 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains BBB, CCC, DDD, EEE
- BGC · beta-D-glucopyranose · sugar · 2 copies
- CL · Chloride ion · ion · chains EEE
- EDO · 1,2-ethanediol · additive · 9 copies · chains AAA, BBB, CCC, DDD, EEE
- GOL · Glycerol · additive · chains CCC, DDD
- PEG · Di(hydroxyethyl)ether · additive · chains EEE
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.51 | 0.79 | 36 | empty |
| 2 | 233 | 0.51 | 0.76 | 31 | EDO |
| 3 | 206 | 0.50 | 0.76 | 28 | EDO |
| 4 | 215 | 0.49 | 0.75 | 30 | EDO |
| 5 | 276 | 0.49 | 0.74 | 35 | empty |
Interfaces
5 interfaces between chains.
- DDD–EEE · 2360 Ų buried · 40 hydrogen bonds · protein-protein
- BBB–CCC · 2353 Ų buried · 42 hydrogen bonds · protein-protein
- CCC–DDD · 2350 Ų buried · 44 hydrogen bonds · protein-protein
- AAA–EEE · 2317 Ų buried · 41 hydrogen bonds · protein-protein
- AAA–BBB · 2303 Ų buried · 42 hydrogen bonds · protein-protein
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 P03089
- Elsewhere: RCSB PDB 7ZIO · PDBe 7ZIO · UniProt P03089
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