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Room-temperature X-ray crystal structure of SARS-cov-2 main protease in complex with narlaprevir
Analyse Room-temperature X-ray crystal structure of SARS-cov-2 main protease in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XQT
- Type
- protein
- Length
- 612 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
- NNA
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 24% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- NNA · (1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl) methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropylamino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.75 | 0.79 | 76 | empty |
| 2 | 273 | 0.56 | 0.77 | 34 | NNA |
| 3 | 310 | 0.51 | 0.73 | 45 | empty |
| 4 | 233 | 0.50 | 0.75 | 30 | NNA |
| 5 | 162 | 0.44 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1682 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6XQT · Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex with… · 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 6XQT · PDBe 6XQT · UniProt P0DTD1
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