Research workbench
Crystal structure of porcine transmissible gastroenteritis virus mpro in complex with an inhibitor N1
Analyse Crystal structure of porcine transmissible gastroenteritis virus mpro in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AMP
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- Q9IW06
- Ligands
- I12
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.-) | protein | 299 | 23% helix, 29% strand | Q9IW06 |
Ligands and binding sites
- I12 · N-[(5-methylisoxazol-3-yl)carbonyl]-L-alanyl-L-valyl-N~1~-((1S)-4-ethoxy-4-oxo-1-{[(3S)-2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.79 | 0.81 | 120 | empty |
| 2 | 451 | 0.66 | 0.79 | 48 | empty |
| 3 | 182 | 0.47 | 0.76 | 29 | I12 |
| 4 | 184 | 0.46 | 0.75 | 28 | I12 |
| 5 | 57 | 0.43 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1409 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2AMP · Crystal Structure Of Porcine Transmissible Gastroenteritis Virus Mpro in Complex with an… · 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 Q9IW06
- Elsewhere: RCSB PDB 2AMP · PDBe 2AMP · UniProt Q9IW06
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