MolNFT v1 · #159896 · protein
Mouse norovirus complexed with tca
6P4K · Capsid protein: “Mouse norovirus complexed with tca”. Electron microscopy, 1 ligand (TCH), 7 pockets (best druggability 0.65). MolNFT v1 #159896 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P4K
- Type
- protein
- Length
- 1,529 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q2V8W4
- Ligands
- TCH
- Pockets
- 7 · best druggability 0.65
Structure
electron microscopy · 3 distinct chains · 4% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 514 | 3% helix, 32% strand | Q2V8W4 |
| B | Capsid protein | protein | 513 | 3% helix, 31% strand | Q2V8W4 |
| C | Capsid protein | protein | 502 | 5% helix, 30% strand | Q2V8W4 |
Ligands and binding sites
- TCH · Taurocholic acid · ligand · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.65 | 0.81 | 51 | empty |
| 2 | 444 | 0.61 | 0.76 | 55 | empty |
| 3 | 298 | 0.60 | 0.78 | 39 | empty |
| 4 | 281 | 0.53 | 0.75 | 28 | empty |
| 5 | 79 | 0.46 | 0.81 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1179 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 883 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 824 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6P4K · mouse norovirus complexed with TCA · 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 Q2V8W4
- Elsewhere: RCSB PDB 6P4K · PDBe 6P4K · UniProt Q2V8W4
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