Research workbench
Crystal structure of P domain from norwalk virus strain vietnam 026 in complex with hbga type ley
Analyse Crystal structure of P domain from norwalk virus strain vietnam 026 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PA2
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- FUC, NAG, GAL
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 315 | 8% helix, 37% strand | Q5F4T5 |
| B | Capsid protein | protein | 310 | 7% helix, 36% strand | Q5F4T5 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- GAL · beta-D-galactopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.75 | 0.82 | 73 | EDO |
| 2 | 168 | 0.64 | 0.85 | 30 | EDO |
| 3 | 424 | 0.64 | 0.78 | 56 | EDO |
| 4 | 180 | 0.52 | 0.79 | 27 | EDO |
| 5 | 99 | 0.37 | 0.75 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1878 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3PA2 · Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA… · 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 Q5F4T5
- Elsewhere: RCSB PDB 3PA2 · PDBe 3PA2 · UniProt Q5F4T5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.