Research workbench
Jc polyomavirus genotype 3 VP1 in complex with GD1A oligosaccharide
Analyse Jc polyomavirus genotype 3 VP1 in complex with GD1A oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X11
- Type
- protein
- Length
- 1,278 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P90498
- Ligands
- SIA, K
- Pockets
- 12 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Major capsid protein | protein | 256 | 8% helix, 43% strand | P90498 |
| E | Major capsid protein | protein | 257 | 8% helix, 42% strand | P90498 |
| A | Major capsid protein | protein | 255 | 8% helix, 40% strand | P90498 |
| D | Major capsid protein | protein | 254 | 7% helix, 43% strand | P90498 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains B, C, E, A
- K · Potassium ion · metal · 6 copies · chains B, E, A, C, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains B, E, A, C
- GOL · Glycerol · additive · 4 copies · chains B, A, E, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.51 | 0.76 | 31 | EDO |
| 2 | 220 | 0.50 | 0.76 | 29 | EDO |
| 3 | 219 | 0.50 | 0.76 | 28 | EDO |
| 4 | 304 | 0.50 | 0.73 | 34 | empty |
| 5 | 214 | 0.50 | 0.76 | 28 | EDO |
Interfaces
5 interfaces between chains.
- B–C · 2359 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2307 Ų buried · 41 hydrogen bonds · protein-protein
- E–A · 2274 Ų buried · 46 hydrogen bonds · protein-protein
- E–D · 2268 Ų buried · 46 hydrogen bonds · protein-protein
- B–A · 2258 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4X11 · JC Polyomavirus genotype 3 VP1 in complex with GD1a oligosaccharide · the same entry in another collection · chain B against B, 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 4X11 · PDBe 4X11 · UniProt P90498
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