MolNFT v1 · #115651 · protein
Crystal structure of murine polyomavirus ra strain VP1 in complex with the GD1A glycan
5CQ0 · Capsid protein VP1: “Crystal structure of murine polyomavirus ra strain VP1 in complex with the GD1A glycan”. X-ray diffraction, 4 ligands (GAL, NGA, SIA), 20 pockets (best druggability 0.71). MolNFT v1 #115651 on GenesisL1: 3D…
- 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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