Research workbench
Crystal structure of P domain from norwalk virus strain vietnam 026 in complex with hbga type a
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
- 3PA1
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- GAL, FUC, A2G
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Capsid protein | protein | 315 | 8% helix, 37% strand | Q5F4T5 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.77 | 0.80 | 120 | EDO |
| 2 | 127 | 0.54 | 0.82 | 26 | EDO |
| 3 | 165 | 0.51 | 0.78 | 23 | EDO |
| 4 | 101 | 0.37 | 0.75 | 17 | empty |
| 5 | 78 | 0.29 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2024 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3PA1 · 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 3PA1 · PDBe 3PA1 · UniProt Q5F4T5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.