Research workbench
Crystal structure of SARS-CoV-2 main protease in complex with cpd-19
Analyse Crystal structure of SARS-CoV-2 main protease in complex with cpd-19 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7GRW
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.92
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase nsp5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- XZX, NA
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.92 · 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 | 301 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- XZX · (2S)-N-(3,5-dichlorophenyl)-2-hydroxypropanamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 10 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 | 942 | 0.77 | 0.80 | 80 | empty |
| 2 | 200 | 0.62 | 0.83 | 43 | DMS |
| 3 | 218 | 0.50 | 0.76 | 29 | DMS, XZX |
| 4 | 261 | 0.49 | 0.74 | 54 | DMS, NA |
| 5 | 182 | 0.45 | 0.75 | 29 | XZX, DMS |
Interfaces
1 interface between chains.
- A–B · 1360 Ų buried · 38 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 7GRW · PDBe 7GRW · UniProt P0DTD1
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