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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 MAT-POS-2e8b2191-10 (Mpro-P2072)
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
- 7GM1
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.939
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- RFR, CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.939 · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 25% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 296 | 25% helix, 30% strand | P0DTD1 |
Ligands and binding sites
- RFR · (4S)-6-chloro-N-{6-[(methanesulfonyl)amino]isoquinolin-4-yl}-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide · ligand · chains A
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 9 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 | 1034 | 0.76 | 0.79 | 89 | DMS |
| 2 | 88 | 0.73 | 0.96 | 29 | DMS |
| 3 | 159 | 0.61 | 0.84 | 31 | DMS |
| 4 | 324 | 0.53 | 0.74 | 49 | DMS |
| 5 | 171 | 0.50 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1479 Ų buried · 35 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 7GM1 · PDBe 7GM1 · UniProt P0DTD1
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