Research workbench
Crystal structure of murine polyomavirus pta strain VP1
Analyse Crystal structure of murine polyomavirus pta strain VP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CPU
- Type
- protein
- Length
- 1,396 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- Q76TX8
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 279 | 8% helix, 39% strand | Q76TX8 |
| B, C, E | VP1 | protein | 278 | 8% helix, 39% strand | Q76TX8 |
| D | VP1 | protein | 283 | 8% helix, 39% strand | Q76TX8 |
Ligands and binding sites
- GOL · Glycerol · additive · 7 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 | 121 | 0.66 | 0.89 | 30 | empty |
| 2 | 125 | 0.66 | 0.89 | 28 | empty |
| 3 | 115 | 0.66 | 0.89 | 29 | empty |
| 4 | 124 | 0.65 | 0.88 | 31 | empty |
| 5 | 105 | 0.63 | 0.88 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2264 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 2247 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2237 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 2231 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2216 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5CPU · Crystal structure of murine polyomavirus PTA strain VP1 · 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 Q76TX8
- Elsewhere: RCSB PDB 5CPU · PDBe 5CPU · UniProt Q76TX8
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