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Crystallization of feline coronavirus mpro with GC376 reveals mechanism of inhibition
Analyse Crystallization of feline coronavirus mpro with GC376 reveals mechanism of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SMV
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- UniProt
- B0LJQ9
- Ligands
- UED
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase | protein | 299 | 24% helix, 29% strand | B0LJQ9 |
Ligands and binding sites
- UED · N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.73 | 0.79 | 74 | empty |
| 2 | 384 | 0.64 | 0.79 | 44 | empty |
| 3 | 338 | 0.64 | 0.80 | 35 | empty |
| 4 | 173 | 0.50 | 0.78 | 28 | UED |
| 5 | 190 | 0.50 | 0.77 | 27 | UED |
Interfaces
1 interface between chains.
- A–B · 1258 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7SMV · Crystallization of feline coronavirus Mpro with GC376 reveals mechanism of inhibition · 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 B0LJQ9
- Elsewhere: RCSB PDB 7SMV · PDBe 7SMV · UniProt B0LJQ9
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