Research workbench
Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with UAW243
Analyse Crystal structure of the SARS-cov-2 (COVID-19) main 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
- 6XFN
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; UAW243
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- UZ7, V1V, APY
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 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 | 304 | 26% helix, 29% strand | P0DTD1 |
| B | UAW243 | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- UZ7 · Phenyl hydrogen carbonate · ligand · chains A, B
- V1V · (2S,3S)-3-amino-2-hydroxyhexanoic acid · ligand · chains A, B
- APY · 2-aminomethyl-pyridine · ligand · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.62 | 0.83 | 27 | V1V, APY |
| 2 | 79 | 0.33 | 0.75 | 14 | empty |
| 3 | 50 | 0.30 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 115 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6XFN · Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with UAW243 · 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 6XFN · PDBe 6XFN · UniProt P0DTD1
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