Research workbench
Protruding domain of GII.17 norovirus KAWASAKI308 in complex with 3- fucosyllactose (3FL)
Analyse Protruding domain of GII.17 norovirus KAWASAKI308 in complex with 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LKK
- Type
- protein
- Length
- 611 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- A0A0S1Z370
- Ligands
- GLC, FUC, GAL, MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein | protein | 305 | 5% helix, 35% strand | A0A0S1Z370 |
| B | Major capsid protein | protein | 306 | 5% helix, 36% strand | A0A0S1Z370 |
Ligands and binding sites
- GLC · 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
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
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 | 725 | 0.78 | 0.82 | 102 | EDO |
| 2 | 135 | 0.67 | 0.88 | 29 | EDO |
| 3 | 91 | 0.42 | 0.79 | 19 | empty |
| 4 | 90 | 0.36 | 0.75 | 19 | empty |
| 5 | 79 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1812 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5LKK · Protruding domain of GII.17 norovirus Kawasaki308 in complex with 3-fucosyllactose (3FL) · 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 A0A0S1Z370
- Elsewhere: RCSB PDB 5LKK · PDBe 5LKK · UniProt A0A0S1Z370
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