Research workbench
Crystal structure of P domain from norovirus GI.9 capsid protein in complex with lewis X antigen.
Analyse Crystal structure of P domain from norovirus GI.9 capsid protein in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VS9
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- F2XMU3
- Ligands
- NDG, FUC, GAL, MG, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | VP1 | protein | 310 | 9% helix, 34% strand | F2XMU3 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.80 | 0.90 | 60 | empty |
| 2 | 129 | 0.76 | 0.95 | 23 | empty |
| 3 | 175 | 0.44 | 0.75 | 28 | empty |
| 4 | 102 | 0.42 | 0.77 | 17 | CL |
| 5 | 102 | 0.41 | 0.77 | 22 | CL |
Interfaces
1 interface between chains.
- A–B · 1696 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7VS9 · Crystal structure of P domain from norovirus GI.9 capsid protein in complex with Lewis x… · 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 F2XMU3
- Elsewhere: RCSB PDB 7VS9 · PDBe 7VS9 · UniProt F2XMU3
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