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Open data
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Basic information
Entry | Database: PDB / ID: 7wqh | ||||||
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Title | Crystal structure of HCoV-NL63 main protease with PF07304814 | ||||||
![]() | 3C-like proteinase | ||||||
![]() | VIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | ![]() host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 ...host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhong, F.L. / Zhou, X.L. / Lin, C. / Zeng, P. / Li, J. / Zhang, J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814 Authors: Li, J. / Lin, C. / Zhou, X. / Zhong, F. / Zeng, P. / McCormick, P.J. / Jiang, H. / Zhang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.3 KB | Display | ![]() |
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PDB format | ![]() | 94.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vvpC ![]() 7wqjC ![]() 7e6lS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32320.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P0C6X5, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium citrate tribasic dihydrate, 16% w/v Polyethylene glycol 3350, pH5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979137 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→59.66 Å / Num. obs: 25391 / % possible obs: 93.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.8932995056 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.32→2.45 Å / Rmerge(I) obs: 0.577 / Num. unique obs: 3867 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7E6L Resolution: 2.32→37.0239 Å / SU ML: 0.334625280692 / Cross valid method: NONE / σ(F): 1.33793583676 / Phase error: 29.6211162422 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.4087182573 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→37.0239 Å
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Refine LS restraints |
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LS refinement shell |
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