Research workbench
1.50 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 2k
Analyse 1.50 A resolution structure of SARS-CoV-2 3CL protease in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LKT
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- Y7M, Y4V
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.5 · 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 | 297 | 26% helix, 30% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- Y7M · (1S,2S)-2-((S)-2-(((adamantan-1-ylmethoxy)carbonyl) amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- Y4V · (1R,2S)-2-((S)-2-(((adamantan-1-ylmethoxy)carbonyl) amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B
- FLC · Citrate anion · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.73 | 0.77 | 61 | empty |
| 2 | 190 | 0.54 | 0.79 | 41 | empty |
| 3 | 184 | 0.53 | 0.79 | 39 | empty |
| 4 | 190 | 0.52 | 0.78 | 26 | Y7M, Y4V |
| 5 | 182 | 0.52 | 0.78 | 24 | Y7M, Y4V |
Interfaces
1 interface between chains.
- A–B · 1030 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7LKT · 1.50 a resolution structure of SARS-cov-2 3CL protease in complex with inhibitor 2K · 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 7LKT · PDBe 7LKT · UniProt P0DTD1
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