Research workbench
Protruding domain of GII.4 human norovirus isolate 8-14 in complex with hbga type B (triglycan)
Analyse Protruding domain of GII.4 human norovirus isolate 8-14 in complex with hbga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LFE
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- M4QNL3
- Ligands
- GLA, FUC
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 309 | 5% helix, 35% strand | M4QNL3 |
| B | VP1 | protein | 306 | 4% helix, 36% strand | M4QNL3 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.75 | 0.95 | 20 | empty |
| 2 | 50 | 0.71 | 0.99 | 25 | empty |
| 3 | 456 | 0.70 | 0.81 | 52 | empty |
| 4 | 469 | 0.70 | 0.80 | 54 | empty |
| 5 | 82 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1779 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5LFE · Protruding domain of GII.4 human norovirus isolate 8-14 in complex with HBGA type B… · 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
- Every structure of UniProt M4QNL3
- Elsewhere: RCSB PDB 5LFE · PDBe 5LFE · UniProt M4QNL3
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