Research workbench
Polyomavirus VP1 pentamer complexed with a disialylated hexasaccharide
Analyse Polyomavirus VP1 pentamer complexed with a disialylated hexasaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VPS
- Type
- protein
- Length
- 1,429 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyomavirus VP1 pentamer
- UniProt
- P49302
- Ligands
- SIA, NAG, GAL
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Polyomavirus VP1 pentamer | protein | 285 | 7% helix, 40% strand | P49302 |
| B | Polyomavirus VP1 pentamer | protein | 289 | 7% helix, 40% strand | P49302 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 10 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, B, C, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.68 | 0.90 | 28 | empty |
| 2 | 108 | 0.67 | 0.91 | 29 | empty |
| 3 | 113 | 0.64 | 0.89 | 29 | empty |
| 4 | 111 | 0.64 | 0.89 | 27 | empty |
| 5 | 101 | 0.63 | 0.89 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2358 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 2350 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 2347 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2347 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2329 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1VPS · Polyomavirus VP1 pentamer complexed with a disialylated hexasaccharide · 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 P49302
- Elsewhere: RCSB PDB 1VPS · PDBe 1VPS · UniProt P49302
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