Research workbench
Crystal structure of main protease of SARS-CoV-2 complexed with inhibitor
Analyse Crystal structure of main protease of SARS-CoV-2 complexed with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9BPF
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase nsp5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- YDL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- YDL · N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.76 | 0.79 | 67 | empty |
| 2 | 228 | 0.54 | 0.78 | 29 | YDL |
| 3 | 240 | 0.52 | 0.76 | 27 | YDL |
| 4 | 161 | 0.44 | 0.75 | 26 | empty |
| 5 | 140 | 0.43 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1618 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 P0DTD1
- Elsewhere: RCSB PDB 9BPF · PDBe 9BPF · UniProt P0DTD1
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