Research workbench
Jc polyomavirus VP1 in complex with lstc
Analyse Jc polyomavirus 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
- 3NXD
- Type
- protein
- Length
- 1,297 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- P03089
- Ligands
- GAL, BGC, NAG, SIA
- Pockets
- 11 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Major capsid protein VP1 | protein | 261 | 8% helix, 41% strand | P03089 |
| B, E | Major capsid protein VP1 | protein | 258 | 8% helix, 41% strand | P03089 |
| A | Major capsid protein VP1 | protein | 259 | 8% helix, 42% strand | P03089 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains C, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, D, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains C, D, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains C, A, D, E
- GOL · Glycerol · additive · 5 copies · chains C, B, A, E, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.54 | 0.78 | 41 | empty |
| 2 | 200 | 0.52 | 0.77 | 41 | empty |
| 3 | 177 | 0.51 | 0.78 | 37 | empty |
| 4 | 314 | 0.51 | 0.73 | 35 | empty |
| 5 | 214 | 0.50 | 0.76 | 29 | EDO |
Interfaces
5 interfaces between chains.
- A–E · 2357 Ų buried · 41 hydrogen bonds · protein-protein
- C–B · 2351 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2346 Ų buried · 46 hydrogen bonds · protein-protein
- B–A · 2336 Ų buried · 45 hydrogen bonds · protein-protein
- D–E · 2320 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 3NXD · JC polyomavirus 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 3NXD · PDBe 3NXD · UniProt P03089
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