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Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with inhibitor UAW246
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
- 6XBG
- Type
- protein
- Length
- 605 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Inhibitor UAW246
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- P6S, UZ4, UZ1, NA
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 26% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 303 | 26% helix, 29% strand | P0DTD1 |
| C, E | Inhibitor UAW246 | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- P6S · benzyl hydrogen carbonate · ligand · 2 copies · chains A, C, B, E
- UZ4 · (2R,3S)-3-amino-2-hydroxy-4-[(3S)-2-oxopyrrolidin-3-yl]butanoic acid · ligand · 2 copies · chains A, C, B, E
- UZ1 · Cyclopropanamine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- GOL · Glycerol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.73 | 0.77 | 63 | GOL |
| 2 | 328 | 0.54 | 0.74 | 45 | GOL |
| 3 | 160 | 0.50 | 0.78 | 32 | empty |
| 4 | 138 | 0.43 | 0.75 | 27 | empty |
| 5 | 94 | 0.37 | 0.76 | 19 | UZ4, UZ1 |
Interfaces
3 interfaces between chains.
- A–B · 1190 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 196 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 190 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6XBG · Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor… · 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 6XBG · PDBe 6XBG · UniProt P0DTD1
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