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Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to H pentasaccharide
Analyse Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SLN
- Type
- protein
- Length
- 3,044 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid
- UniProt
- Q5EGK8
- Ligands
- GAL, BGC, NAG, FUC
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid | protein | 309 | 3% helix, 35% strand | Q5EGK8 |
| B, F, G | Capsid | protein | 308 | 6% helix, 36% strand | Q5EGK8 |
| C | Capsid | protein | 311 | 5% helix, 35% strand | Q5EGK8 |
| D, J | Capsid | protein | 307 | 4% helix, 37% strand | Q5EGK8 |
| E | Capsid | protein | 309 | 5% helix, 36% strand | Q5EGK8 |
| H | Capsid | protein | 292 | 5% helix, 34% strand | Q5EGK8 |
| I | Capsid | protein | 285 | 6% helix, 34% strand | Q5EGK8 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 16 copies · chains C, E, A, F, D, B, J, G
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains C, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, E, A, F, D, B, J, G
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains A, C, B, E, D, F, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.75 | 0.77 | 101 | empty |
| 2 | 66 | 0.74 | 0.98 | 20 | empty |
| 3 | 682 | 0.74 | 0.80 | 64 | empty |
| 4 | 66 | 0.74 | 0.98 | 21 | empty |
| 5 | 67 | 0.74 | 0.98 | 21 | empty |
Interfaces
13 interfaces between chains.
- G–J · 1633 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1611 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1593 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1589 Ų buried · 19 hydrogen bonds · protein-protein
- B–J · 785 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3SLN · Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to H… · 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 Q5EGK8
- Elsewhere: RCSB PDB 3SLN · PDBe 3SLN · UniProt Q5EGK8
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