Research workbench
The crystal structure of SARS-cov-2 main protease in complex with GC376
Analyse The crystal structure of SARS-cov-2 main protease in complex with GC376 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CBT
- Type
- protein
- Length
- 596 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- K36
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 298 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- K36 · (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.76 | 0.78 | 90 | empty |
| 2 | 310 | 0.56 | 0.76 | 43 | empty |
| 3 | 206 | 0.52 | 0.77 | 29 | K36 |
| 4 | 180 | 0.50 | 0.77 | 26 | K36 |
| 5 | 167 | 0.46 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1052 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7CBT · The crystal structure of SARS-CoV-2 main protease in complex with GC376 · the same entry in another collection · chain A against A, TM-score 1.00
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 7CBT · PDBe 7CBT · UniProt P0DTD1
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