Research workbench
Crystal structure of capsid P domain of norovirus GI.3 dsv complexed with NA2 N-glycan
Analyse Crystal structure of capsid P domain of norovirus GI.3 dsv complexed with NA2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EQW
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid P domain
- Ligands
- MAN, NAG, GAL
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid P domain | protein | 304 | 10% helix, 31% strand | — |
| B | Capsid P domain | protein | 296 | 9% helix, 31% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar
- GAL · beta-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.83 | 0.90 | 57 | empty |
| 2 | 62 | 0.73 | 0.99 | 20 | empty |
| 3 | 72 | 0.46 | 0.83 | 23 | empty |
| 4 | 180 | 0.45 | 0.75 | 26 | empty |
| 5 | 189 | 0.45 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1577 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7EQW · Crystal structure of capsid P domain of norovirus GI.3 DSV complexed with NA2 N-glycan · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 7EQW · PDBe 7EQW
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