MolNFT v1 · #108663 · protein
Jc polyomavirus VP1 five-fold pore mutant P223M
4WE0 · Major capsid protein VP1: “Jc polyomavirus VP1 five-fold pore mutant P223M”. X-ray diffraction, 16 pockets (best druggability 0.58). MolNFT v1 #108663 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WE0
- Type
- protein
- Length
- 1,288 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- P03089
- Pockets
- 16 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein VP1 | protein | 259 | 8% helix, 42% strand | P03089 |
| B, E | Major capsid protein VP1 | protein | 258 | 8% helix, 42% strand | P03089 |
| C | Major capsid protein VP1 | protein | 256 | 8% helix, 42% strand | P03089 |
| D | Major capsid protein VP1 | protein | 257 | 8% helix, 42% strand | P03089 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, E, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.58 | 0.75 | 43 | EDO |
| 2 | 224 | 0.54 | 0.78 | 41 | empty |
| 3 | 253 | 0.54 | 0.77 | 42 | empty |
| 4 | 76 | 0.53 | 0.86 | 20 | empty |
| 5 | 281 | 0.53 | 0.75 | 45 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2391 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 2391 Ų buried · 47 hydrogen bonds · protein-protein
- A–E · 2371 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2369 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2358 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 4WE0 · JC Polyomavirus VP1 five-fold pore mutant P223M · 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 4WE0 · PDBe 4WE0 · UniProt P03089
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