MolNFT v1 · #78810 · protein
Structural characterization of a GII.4 2004 norovirus variant (TCH05)
3SKB · Capsid: “Structural characterization of a GII.4 2004 norovirus variant (TCH05)”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #78810 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SKB
- Type
- protein
- Length
- 3,041 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid
- UniProt
- Q5EGK8
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, G, H | Capsid | protein | 308 | 4% helix, 36% strand | Q5EGK8 |
| B, E, F | Capsid | protein | 309 | 4% helix, 36% strand | Q5EGK8 |
| I | Capsid | protein | 291 | 4% helix, 35% strand | Q5EGK8 |
| J | Capsid | protein | 283 | 5% helix, 34% strand | Q5EGK8 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.73 | 0.80 | 55 | empty |
| 2 | 1178 | 0.73 | 0.76 | 91 | empty |
| 3 | 753 | 0.72 | 0.78 | 79 | empty |
| 4 | 61 | 0.72 | 0.97 | 21 | empty |
| 5 | 59 | 0.71 | 0.98 | 21 | empty |
Interfaces
13 interfaces between chains.
- C–H · 1637 Ų buried · 22 hydrogen bonds · protein-protein
- D–G · 1605 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1595 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 1563 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 674 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3SKB · Structural characterization of a GII.4 2004 norovirus variant (TCH05) · 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 3SKB · PDBe 3SKB · UniProt Q5EGK8
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