Research workbench
S268Y variant of jc polyomavirus major capsid protein VP1
Analyse S268Y variant of jc polyomavirus major capsid protein VP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JCD
- Type
- protein
- Length
- 1,285 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- P03089
- Pockets
- 15 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Major capsid protein VP1 | protein | 257 | 8% helix, 42% strand | P03089 |
| B | Major capsid protein VP1 | protein | 258 | 8% helix, 42% strand | P03089 |
| C | Major capsid protein VP1 | protein | 256 | 9% helix, 42% strand | P03089 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, E, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.51 | 0.74 | 35 | empty |
| 2 | 213 | 0.51 | 0.76 | 30 | empty |
| 3 | 233 | 0.50 | 0.75 | 28 | EDO |
| 4 | 139 | 0.50 | 0.80 | 28 | empty |
| 5 | 191 | 0.50 | 0.77 | 40 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2366 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 2353 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2329 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 2322 Ų buried · 49 hydrogen bonds · protein-protein
- A–E · 2320 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4JCD · S268Y Variant of JC Polyomavirus Major Capsid Protein 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 P03089
- Elsewhere: RCSB PDB 4JCD · PDBe 4JCD · UniProt P03089
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