Research workbench
Crystal structure of SARS coronavirus main protease in complex with Baicalei
Analyse Crystal structure of SARS coronavirus main protease in complex with Baicalei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XAX
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase nsp5
- EC
- 3.4.22.69
- UniProt
- P0C6U8
- Ligands
- 3WL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.25 · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 298 | 25% helix, 30% strand | P0C6U8 |
| B | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 296 | 25% helix, 30% strand | P0C6U8 |
Ligands and binding sites
- 3WL · 5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one · ligand · chains A
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 | 827 | 0.73 | 0.78 | 59 | empty |
| 2 | 218 | 0.55 | 0.78 | 39 | empty |
| 3 | 152 | 0.48 | 0.77 | 28 | empty |
| 4 | 188 | 0.43 | 0.73 | 36 | empty |
| 5 | 152 | 0.42 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1008 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 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 P0C6U8
- Elsewhere: RCSB PDB 7XAX · PDBe 7XAX · UniProt P0C6U8
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