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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-2e8b2191-12 (Mpro-P2074)
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
- 7GM2
- Type
- protein
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.891
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- RG3, CL
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.891 · 2 distinct chains · 25% helix, 29% 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 | 298 | 25% helix, 30% strand | P0DTD1 |
Ligands and binding sites
- RG3 · (4S)-6-chloro-N-[7-(methanesulfonyl)isoquinolin-4-yl]-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide · ligand · 2 copies · chains A, B
- 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.76 | 0.79 | 87 | DMS |
| 2 | 71 | 0.72 | 0.96 | 21 | DMS |
| 3 | 130 | 0.59 | 0.84 | 30 | DMS |
| 4 | 315 | 0.54 | 0.75 | 45 | DMS |
| 5 | 234 | 0.53 | 0.76 | 28 | RG3 |
Interfaces
1 interface between chains.
- A–B · 1481 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 7GM2 · PDBe 7GM2 · UniProt P0DTD1
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