Research workbench
Jc polyomavirus genotype 3 VP1 in complex with GM1 oligosaccharide
Analyse Jc polyomavirus genotype 3 VP1 in complex with GM1 oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X0Z
- Type
- protein
- Length
- 1,286 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P90498
- Ligands
- GAL, NGA, SIA, BGC, K
- Pockets
- 11 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Major capsid protein | protein | 258 | 8% helix, 42% strand | P90498 |
| B, D | Major capsid protein | protein | 257 | 8% helix, 42% strand | P90498 |
| C | Major capsid protein | protein | 256 | 8% helix, 41% strand | P90498 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C, D
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains B, C, D
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains B, C, D, E
- BGC · beta-D-glucopyranose · sugar
- K · Potassium ion · metal · 10 copies · chains A, E, B, C, D
- GOL · Glycerol · additive · 22 copies · chains A, E, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.52 | 0.82 | 28 | GOL |
| 2 | 127 | 0.51 | 0.81 | 28 | GOL |
| 3 | 120 | 0.50 | 0.81 | 25 | K, GOL |
| 4 | 219 | 0.50 | 0.75 | 30 | EDO |
| 5 | 165 | 0.49 | 0.78 | 36 | GOL |
Interfaces
5 interfaces between chains.
- D–E · 2344 Ų buried · 48 hydrogen bonds · protein-protein
- A–E · 2344 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2332 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 2330 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2310 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4X0Z · JC Polyomavirus genotype 3 VP1 in complex with GM1 oligosaccharide · 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 P90498
- Elsewhere: RCSB PDB 4X0Z · PDBe 4X0Z · UniProt P90498
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