Research workbench
Jc polyomavirus genotype 3 VP1 in complex with GM2 oligosaccharide
Analyse Jc polyomavirus genotype 3 VP1 in complex with GM2 oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X10
- Type
- protein
- Length
- 1,288 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P90498
- Ligands
- GAL, SIA, NGA, BGC, K
- Pockets
- 11 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Major capsid protein | protein | 258 | 8% helix, 42% strand | P90498 |
| B | Major capsid protein | protein | 257 | 8% helix, 42% strand | P90498 |
| C | Major capsid protein | protein | 257 | 8% helix, 41% strand | P90498 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 3 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains B, C, D, E
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains B, C, D
- BGC · beta-D-glucopyranose · sugar · 2 copies
- K · Potassium ion · metal · 7 copies · chains A, E, B, C, D
- GOL · Glycerol · additive · 15 copies · chains A, E, B, C, D
- EDO · 1,2-ethanediol · additive · 6 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.54 | 0.81 | 37 | GOL, K |
| 2 | 116 | 0.54 | 0.83 | 25 | empty |
| 3 | 110 | 0.52 | 0.82 | 27 | empty |
| 4 | 170 | 0.51 | 0.78 | 38 | GOL |
| 5 | 225 | 0.50 | 0.75 | 29 | GOL |
Interfaces
5 interfaces between chains.
- D–E · 2377 Ų buried · 43 hydrogen bonds · protein-protein
- A–E · 2359 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2356 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2340 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2322 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 4X10 · JC Polyomavirus genotype 3 VP1 in complex with GM2 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 4X10 · PDBe 4X10 · UniProt P90498
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