Research workbench
Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens
Analyse Unraveling the role of the secretor antigen in human rotavirus attachment to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HA0
- Type
- protein
- Length
- 322 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Rotavirus A
- Molecule
- Outer capsid protein VP4
- UniProt
- A0A0S0VKY7
- Ligands
- NAG, GAL, FUC
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · resolution 1.85 · 2 distinct chains · 8% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer capsid protein VP4 | protein | 162 | 8% helix, 55% strand | A0A0S0VKY7 |
| B | Outer capsid protein VP4 | protein | 160 | 8% helix, 58% strand | A0A0S0VKY7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.62 | 0.82 | 28 | empty |
| 2 | 156 | 0.50 | 0.79 | 22 | empty |
| 3 | 76 | 0.32 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 685 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6HA0 · Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood… · 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 A0A0S0VKY7
- Elsewhere: RCSB PDB 6HA0 · PDBe 6HA0 · UniProt A0A0S0VKY7
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