Research workbench
Crystal structures of P domain of norovirus VA387 in complex with blood group trisaccharides type B
Analyse Crystal structures of P domain of norovirus VA387 in complex with blood group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OBT
- Type
- protein
- Length
- 307 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q913Z3
- Ligands
- GAL, FUC, GLA
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 307 | 6% helix, 35% strand | Q913Z3 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- GLA · alpha-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.40 | 0.81 | 20 | empty |
| 2 | 80 | 0.37 | 0.77 | 16 | empty |
Compared structures
- 2OBT · Crystal Structures of P Domain of Norovirus VA387 in Complex with Blood Group… · 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 Q913Z3
- Elsewhere: RCSB PDB 2OBT · PDBe 2OBT · UniProt Q913Z3
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