Research workbench
Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)
Analyse Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N7M
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- Q83884
- Ligands
- GLC, GAL, FUC, NA
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 288 | 8% helix, 31% strand | Q83884 |
| B | Capsid protein VP1 | protein | 288 | 9% helix, 32% strand | Q83884 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.77 | 0.84 | 79 | empty |
| 2 | 202 | 0.51 | 0.77 | 36 | EDO |
Interfaces
1 interface between chains.
- A–B · 1604 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5N7M · Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL) · 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 Q83884
- Elsewhere: RCSB PDB 5N7M · PDBe 5N7M · UniProt Q83884
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