Research workbench
Jc polyomavirus genotype 3 VP1 in complex with lstc pentasaccharide
Analyse Jc polyomavirus genotype 3 VP1 in complex with lstc pentasaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X13
- Type
- protein
- Length
- 1,285 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P90498
- Ligands
- GAL, NAG, SIA, BGC, K
- Pockets
- 11 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Major capsid protein | protein | 258 | 8% helix, 41% strand | P90498 |
| B, D | Major capsid protein | protein | 256 | 8% helix, 43% strand | P90498 |
| C | Major capsid protein | protein | 257 | 8% helix, 41% strand | P90498 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains B, C, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, C, D, A, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains B, C, D, A, E
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains B, C
- K · Potassium ion · metal · 5 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 11 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.50 | 0.76 | 29 | GOL |
| 2 | 216 | 0.49 | 0.75 | 29 | GOL |
| 3 | 218 | 0.49 | 0.75 | 31 | EDO |
| 4 | 141 | 0.49 | 0.79 | 32 | empty |
| 5 | 273 | 0.49 | 0.74 | 35 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2302 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2294 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 2287 Ų buried · 48 hydrogen bonds · protein-protein
- A–E · 2280 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 2247 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 4X13 · JC Polyomavirus genotype 3 VP1 in complex with LSTc pentasaccharide · 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 P90498
- Elsewhere: RCSB PDB 4X13 · PDBe 4X13 · UniProt P90498
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.