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Crystals structure of the SARS-cov-2 (COVID-19) main protease with inhibitor gc-376
Analyse Crystals structure of the SARS-cov-2 (COVID-19) main protease with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WTT
- Type
- protein
- Length
- 906 residues
- Chains
- 3
- 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, B1S, MG, CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3C-like proteinase (EC 3.4.22.69) | protein | 302 | 25% helix, 28% 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, C
- B1S · (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.79 | 0.81 | 132 | CL, MG |
| 2 | 919 | 0.77 | 0.80 | 87 | empty |
| 3 | 193 | 0.54 | 0.79 | 27 | B1S |
| 4 | 193 | 0.50 | 0.77 | 28 | K36 |
| 5 | 191 | 0.49 | 0.76 | 28 | K36 |
Interfaces
2 interfaces between chains.
- B–C · 1404 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 893 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6WTT · Crystals Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor GC-376 · the same entry in another collection · chain C against C, 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 6WTT · PDBe 6WTT · UniProt P0DTD1
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