[English] 日本語
![](img/lk-miru.gif)
- PDB-7en9: Crystal structure of SARS-CoV-2 3CLpro in complex with the non-co... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7en9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-02 | ||||||
![]() | 3C-like proteinase | ||||||
![]() | VIRAL PROTEIN / Non-covalent / Inhibitor / 3CLpro / Coronavirus | ||||||
Function / homology | ![]() viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hou, N. / Peng, C. / Hu, Q. | ||||||
![]() | ![]() Title: Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro. Authors: Hou, N. / Shuai, L. / Zhang, L. / Xie, X. / Tang, K. / Zhu, Y. / Yu, Y. / Zhang, W. / Tan, Q. / Zhong, G. / Wen, Z. / Wang, C. / He, X. / Huo, H. / Gao, H. / Xu, Y. / Xue, J. / Peng, C. / ...Authors: Hou, N. / Shuai, L. / Zhang, L. / Xie, X. / Tang, K. / Zhu, Y. / Yu, Y. / Zhang, W. / Tan, Q. / Zhong, G. / Wen, Z. / Wang, C. / He, X. / Huo, H. / Gao, H. / Xu, Y. / Xue, J. / Peng, C. / Zou, J. / Schindewolf, C. / Menachery, V. / Su, W. / Yuan, Y. / Shen, Z. / Zhang, R. / Yuan, S. / Yu, H. / Shi, P.Y. / Bu, Z. / Huang, J. / Hu, Q. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 59 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 821.1 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7en8C ![]() 7endC ![]() 7eneC ![]() 6y2eS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0DTC1, SARS coronavirus main proteinase |
---|---|
#2: Chemical | ChemComp-J7O / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.01 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.05 M citric acid, 0.05 M BIS-TRIS propane pH 5.0, 16% w/v polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.68 Å / Num. obs: 29294 / % possible obs: 99.61 % / Redundancy: 4.8 % / Biso Wilson estimate: 21.01 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.1339 / Rpim(I) all: 0.06396 / Rrim(I) all: 0.1488 / Net I/σ(I): 18.24 |
Reflection shell | Resolution: 1.9→1.968 Å / Rmerge(I) obs: 0.3152 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 2916 / CC1/2: 0.861 / Rpim(I) all: 0.2016 / Rrim(I) all: 0.3763 / % possible all: 99.08 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6Y2E Resolution: 1.9→29.68 Å / SU ML: 0.2123 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6425 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.68 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|