Research workbench
Crystal structure of murine polyomavirus ra strain VP1 in complex with the GD1A glycan
Analyse Crystal structure of murine polyomavirus ra strain VP1 in complex with the GD1A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CQ0
- Type
- protein
- Length
- 1,400 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- P49302
- Ligands
- GAL, NGA, SIA, SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 281 | 8% helix, 39% strand | P49302 |
| B | Capsid protein VP1 | protein | 279 | 8% helix, 39% strand | P49302 |
| C, E | Capsid protein VP1 | protein | 278 | 8% helix, 40% strand | P49302 |
| D | Capsid protein VP1 | protein | 284 | 8% helix, 38% strand | P49302 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains A, B, C, D, E
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 5 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 21 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.71 | 0.95 | 26 | empty |
| 2 | 125 | 0.67 | 0.89 | 30 | empty |
| 3 | 112 | 0.66 | 0.90 | 27 | empty |
| 4 | 104 | 0.65 | 0.90 | 26 | empty |
| 5 | 108 | 0.64 | 0.89 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2255 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 2248 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2244 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 2239 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2227 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5CQ0 · Crystal structure of murine polyomavirus RA strain VP1 in complex with the GD1a glycan · 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 5CQ0 · PDBe 5CQ0 · UniProt P49302
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