MolNFT v1 · #108661 · protein
Jc polyomavirus VP1 five-fold pore mutant N221Q
4WDY · Major capsid protein VP1: “Jc polyomavirus VP1 five-fold pore mutant N221Q”. X-ray diffraction, 12 pockets (best druggability 0.60). MolNFT v1 #108661 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WDY
- Type
- protein
- Length
- 1,291 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- P03089
- Pockets
- 12 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Major capsid protein VP1 | protein | 258 | 8% helix, 42% strand | P03089 |
| C | Major capsid protein VP1 | protein | 258 | 8% helix, 42% strand | P03089 |
| D | Major capsid protein VP1 | protein | 259 | 7% helix, 43% strand | P03089 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, E, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.60 | 0.75 | 35 | empty |
| 2 | 240 | 0.52 | 0.76 | 42 | empty |
| 3 | 184 | 0.51 | 0.78 | 41 | empty |
| 4 | 222 | 0.50 | 0.76 | 33 | empty |
| 5 | 218 | 0.50 | 0.75 | 29 | EDO |
Interfaces
5 interfaces between chains.
- C–D · 2375 Ų buried · 43 hydrogen bonds · protein-protein
- A–E · 2367 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 2360 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2345 Ų buried · 45 hydrogen bonds · protein-protein
- D–E · 2344 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4WDY · JC Polyomavirus VP1 five-fold pore mutant N221Q · 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 P03089
- Elsewhere: RCSB PDB 4WDY · PDBe 4WDY · UniProt P03089
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