Research workbench
Protruding domain of GII.4 human norovirus NSW0514 in complex with 2- fucosyllactose (2'FL)
Analyse Protruding domain of GII.4 human norovirus NSW0514 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
- 5J35
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- K4LM89
- Ligands
- GLC, GAL, FUC
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | VP1 | protein | 309 | 6% helix, 35% strand | K4LM89 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.75 | 0.95 | 21 | empty |
| 2 | 59 | 0.73 | 0.98 | 19 | empty |
| 3 | 541 | 0.70 | 0.80 | 54 | EDO |
| 4 | 537 | 0.70 | 0.80 | 56 | empty |
| 5 | 70 | 0.51 | 0.85 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1745 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5J35 · Protruding domain of GII.4 human norovirus NSW0514 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 K4LM89
- Elsewhere: RCSB PDB 5J35 · PDBe 5J35 · UniProt K4LM89
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