MolNFT v1 · #78848 · protein
Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to a trisaccharide
3SLD · Capsid: “Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to a trisaccharide”. X-ray diffraction, 3 ligands (GAL, FUC, A2G), 20 pockets (best druggability 0.81). MolNFT v1 #78848 on GenesisL1: 3D…
- PDB
- 3SLD
- Type
- protein
- Length
- 3,046 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid
- UniProt
- Q5EGK8
- Ligands
- GAL, FUC, A2G
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid | protein | 309 | 5% helix, 35% strand | Q5EGK8 |
| B, F, G | Capsid | protein | 308 | 5% helix, 35% strand | Q5EGK8 |
| C | Capsid | protein | 311 | 5% helix, 34% strand | Q5EGK8 |
| D, J | Capsid | protein | 307 | 5% helix, 36% strand | Q5EGK8 |
| E | Capsid | protein | 309 | 4% helix, 35% strand | Q5EGK8 |
| H | Capsid | protein | 293 | 6% helix, 34% strand | Q5EGK8 |
| I | Capsid | protein | 286 | 7% helix, 32% strand | Q5EGK8 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains C, E, A, F, B, D, J, G
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains A, C, B, E, D, F, G, J
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · 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 | 1042 | 0.81 | 0.82 | 107 | empty |
| 2 | 75 | 0.75 | 0.98 | 21 | empty |
| 3 | 1173 | 0.74 | 0.77 | 96 | empty |
| 4 | 70 | 0.74 | 0.98 | 20 | empty |
| 5 | 62 | 0.73 | 0.98 | 22 | empty |
Interfaces
13 interfaces between chains.
- G–J · 1610 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1598 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1580 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1573 Ų buried · 15 hydrogen bonds · protein-protein
- B–J · 781 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3SLD · Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to A… · 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 3SLD · PDBe 3SLD · UniProt Q5EGK8
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