Research workbench
S268F variant of jc polyomavirus major capsid protein VP1 in complex with lstc
Analyse S268F variant of jc polyomavirus major capsid protein VP1 in complex with lstc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JCF
- Type
- protein
- Length
- 1,287 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- P03089
- Ligands
- NAG, GAL, SIA
- Pockets
- 12 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Major capsid protein VP1 | protein | 256 | 8% helix, 41% strand | P03089 |
| A | Major capsid protein VP1 | protein | 258 | 8% helix, 42% strand | P03089 |
| B | Major capsid protein VP1 | protein | 259 | 8% helix, 42% strand | P03089 |
| D, E | Major capsid protein VP1 | protein | 257 | 8% helix, 42% strand | P03089 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C, D
- GAL · beta-D-galactopyranose · sugar · chains C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains C, D
- GOL · Glycerol · additive · 5 copies · chains C, B, A, E, D
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.60 | 0.76 | 62 | empty |
| 2 | 321 | 0.51 | 0.74 | 35 | empty |
| 3 | 229 | 0.50 | 0.75 | 29 | empty |
| 4 | 211 | 0.49 | 0.76 | 30 | empty |
| 5 | 159 | 0.49 | 0.78 | 35 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2357 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2340 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2331 Ų buried · 46 hydrogen bonds · protein-protein
- C–B · 2316 Ų buried · 45 hydrogen bonds · protein-protein
- A–E · 2308 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 4JCF · S268F Variant of JC Polyomavirus Major Capsid Protein VP1 in Complex with LSTc · the same entry in another collection · chain C against C, 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 4JCF · PDBe 4JCF · UniProt P03089
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.