MolNFT v1 · #109375 · protein
Jc polyomavirus VP1 from a genotype 3 strain
4X0Y · Major capsid protein: “Jc polyomavirus VP1 from a genotype 3 strain”. X-ray diffraction, 1 ligand (K), 11 pockets (best druggability 0.50). MolNFT v1 #109375 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4X0Y
- Type
- protein
- Length
- 1,288 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P90498
- Ligands
- K
- Pockets
- 11 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein | protein | 258 | 8% helix, 42% strand | P90498 |
| B, C, D | Major capsid protein | protein | 257 | 8% helix, 41% strand | P90498 |
| E | Major capsid protein | protein | 259 | 8% helix, 42% strand | P90498 |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.50 | 0.75 | 30 | EDO |
| 2 | 319 | 0.50 | 0.73 | 32 | empty |
| 3 | 203 | 0.50 | 0.76 | 31 | EDO |
| 4 | 213 | 0.49 | 0.76 | 29 | GOL |
| 5 | 208 | 0.49 | 0.76 | 29 | EDO |
Interfaces
5 interfaces between chains.
- D–E · 2322 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2319 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 2285 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 2277 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2265 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4X0Y · JC polyomavirus VP1 from a genotype 3 strain · 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 P90498
- Elsewhere: RCSB PDB 4X0Y · PDBe 4X0Y · UniProt P90498
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