Research workbench
Group deposition SARS-CoV-2 main protease in complex with inhibitors from the COVID Moonshot -- Crystal Structure of SARS-CoV-2 main protease in complex with VLA-UNK-82501c2c-1 (Mpro-P0153)
Analyse Group deposition SARS-CoV-2 main protease in complex with inhibitors from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7GJ1
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- QJR, CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.95 · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 25% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- QJR · 2-(3,4-dichlorophenyl)-N-(2,7-naphthyridin-4-yl)acetamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 12 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.76 | 0.79 | 79 | DMS |
| 2 | 75 | 0.69 | 0.95 | 28 | DMS |
| 3 | 81 | 0.61 | 0.89 | 19 | DMS |
| 4 | 348 | 0.53 | 0.73 | 50 | DMS |
| 5 | 189 | 0.49 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1474 Ų buried · 37 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 7GJ1 · PDBe 7GJ1 · UniProt P0DTD1
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