MolNFT v1 · #108662 · protein
Jc polyomavirus VP1 five-fold pore mutant N221W
4WDZ · Major capsid protein VP1: “Jc polyomavirus VP1 five-fold pore mutant N221W”. X-ray diffraction, 18 pockets (best druggability 0.58). MolNFT v1 #108662 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WDZ
- Type
- protein
- Length
- 1,290 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- P03089
- Pockets
- 18 · best druggability 0.58
Structure
x-ray diffraction · 3 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, D, E | Major capsid protein VP1 | protein | 258 | 8% helix, 42% strand | P03089 |
| C | Major capsid protein VP1 | protein | 257 | 8% helix, 42% strand | P03089 |
Ligands and binding sites
- GOL · Glycerol · additive · 14 copies · chains A, E, B, C, D
- EDO · 1,2-ethanediol · 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
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.58 | 0.74 | 32 | empty |
| 2 | 72 | 0.56 | 0.88 | 21 | GOL |
| 3 | 72 | 0.55 | 0.87 | 20 | GOL |
| 4 | 63 | 0.54 | 0.88 | 19 | GOL |
| 5 | 71 | 0.54 | 0.86 | 21 | GOL |
Interfaces
5 interfaces between chains.
- D–E · 2399 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2394 Ų buried · 47 hydrogen bonds · protein-protein
- A–E · 2388 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 2386 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2382 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 4WDZ · JC Polyomavirus VP1 five-fold pore mutant N221W · 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 4WDZ · PDBe 4WDZ · UniProt P03089
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