Research workbench
Protruding domain of GII.17 norovirus KAWASAKI308 in complex with 2- fucosyllactose (2'FL)
Analyse Protruding domain of GII.17 norovirus KAWASAKI308 in complex with 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LKG
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- A0A0E4B1P1
- Ligands
- GLC, GAL, FUC, MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 308 | 6% helix, 34% strand | A0A0E4B1P1 |
| B | Capsid protein VP1 | protein | 307 | 6% helix, 35% strand | A0A0E4B1P1 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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 | 770 | 0.78 | 0.82 | 115 | empty |
| 2 | 138 | 0.67 | 0.88 | 29 | empty |
| 3 | 98 | 0.43 | 0.78 | 18 | empty |
| 4 | 74 | 0.37 | 0.77 | 25 | empty |
| 5 | 69 | 0.29 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1869 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5LKG · Protruding domain of GII.17 norovirus Kawasaki308 in complex with 2-fucosyllactose (2'FL) · 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 A0A0E4B1P1
- Elsewhere: RCSB PDB 5LKG · PDBe 5LKG · UniProt A0A0E4B1P1
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