MolNFT v1 · #78623 · protein
Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to secretor lewis hbga (leb)
3SEJ · Capsid: “Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to secretor lewis hbga (leb)”. X-ray diffraction, 4 ligands (GAL, FUC, BGC), 20 pockets (best druggability 0.80). MolNFT v1 #78623 on GenesisL1: 3D…
- PDB
- 3SEJ
- Type
- protein
- Length
- 3,050 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid
- UniProt
- Q5EGK8
- Ligands
- GAL, FUC, BGC, NAG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 5% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid | protein | 309 | 4% helix, 36% strand | Q5EGK8 |
| B | Capsid | protein | 307 | 4% helix, 36% strand | Q5EGK8 |
| C | Capsid | protein | 311 | 5% helix, 35% strand | Q5EGK8 |
| D, J | Capsid | protein | 307 | 5% helix, 36% strand | Q5EGK8 |
| E | Capsid | protein | 309 | 4% helix, 37% strand | Q5EGK8 |
| F, G | Capsid | protein | 308 | 4% helix, 36% strand | Q5EGK8 |
| H | Capsid | protein | 300 | 5% helix, 35% strand | Q5EGK8 |
| I | Capsid | protein | 284 | 5% helix, 30% strand | Q5EGK8 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 16 copies · chains B, C, A, D, E, F, G, J
- FUC · alpha-L-fucopyranose · sugar · 16 copies · chains B, E, A, C, D, F, G, J
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains C, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, C, D, E, 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 | 887 | 0.80 | 0.82 | 114 | empty |
| 2 | 730 | 0.74 | 0.80 | 66 | empty |
| 3 | 769 | 0.74 | 0.79 | 82 | empty |
| 4 | 66 | 0.73 | 0.97 | 19 | empty |
| 5 | 58 | 0.72 | 0.98 | 20 | empty |
Interfaces
13 interfaces between chains.
- G–J · 1621 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1620 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1619 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1598 Ų buried · 18 hydrogen bonds · protein-protein
- B–J · 758 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3SEJ · Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to Secretor… · 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 3SEJ · PDBe 3SEJ · UniProt Q5EGK8
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