Research workbench
Structure of new jersey polyomavirus VP1 in complex with 3'- sialyllactose
Analyse Structure of new jersey polyomavirus VP1 in complex with 3'- sialyllactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y5Y
- Type
- protein
- Length
- 2,791 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- A0A024B5J2
- Ligands
- GAL, SIA, BGC, GLC, MG
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 8 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 279 | 10% helix, 38% strand | A0A024B5J2 |
| B | VP1 | protein | 283 | 10% helix, 38% strand | A0A024B5J2 |
| C, E | VP1 | protein | 281 | 10% helix, 38% strand | A0A024B5J2 |
| D | VP1 | protein | 285 | 9% helix, 39% strand | A0A024B5J2 |
| F, J | VP1 | protein | 274 | 10% helix, 38% strand | A0A024B5J2 |
| G | VP1 | protein | 285 | 9% helix, 39% strand | A0A024B5J2 |
| H | VP1 | protein | 274 | 10% helix, 38% strand | A0A024B5J2 |
| I | VP1 | protein | 275 | 10% helix, 39% strand | A0A024B5J2 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- BGC · beta-D-glucopyranose · sugar · 6 copies
- GLC · alpha-D-glucopyranose · sugar · 4 copies
- MG · Magnesium ion · metal · 10 copies · chains A, B, E, C, D, F, J, G, H, I
- GOL · Glycerol · additive · 39 copies · chains A, E, B, C, D, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.69 | 0.75 | 79 | GOL |
| 2 | 475 | 0.64 | 0.77 | 60 | GOL |
| 3 | 374 | 0.61 | 0.77 | 51 | GOL |
| 4 | 272 | 0.56 | 0.77 | 32 | GOL |
| 5 | 199 | 0.55 | 0.79 | 31 | GOL |
Interfaces
17 interfaces between chains.
- H–I · 2217 Ų buried · 36 hydrogen bonds · protein-protein
- F–G · 2207 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 2207 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2199 Ų buried · 34 hydrogen bonds · protein-protein
- I–J · 2185 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6Y5Y · Structure of New Jersey Polyomavirus VP1 in complex with 3'-Sialyllactose · 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 A0A024B5J2
- Elsewhere: RCSB PDB 6Y5Y · PDBe 6Y5Y · UniProt A0A024B5J2
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