Research workbench
Crystal structure of SARS-CoV-2 main protease in complex with cpd-4
Analyse Crystal structure of SARS-CoV-2 main protease in complex with cpd-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7GRH
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.87
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase nsp5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- Y25, NA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.87 · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 301 | 25% helix, 30% strand | P0DTD1 |
| B | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 306 | 25% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- Y25 · 5-chloropyridin-3-ol · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · 18 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.78 | 0.80 | 84 | DMS |
| 2 | 134 | 0.59 | 0.84 | 30 | DMS |
| 3 | 346 | 0.54 | 0.74 | 49 | DMS |
| 4 | 196 | 0.49 | 0.76 | 28 | Y25 |
| 5 | 204 | 0.47 | 0.75 | 28 | DMS, Y25 |
Interfaces
1 interface between chains.
- A–B · 1526 Ų buried · 43 hydrogen bonds · protein-protein
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 7GRH · PDBe 7GRH · UniProt P0DTD1
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