[English] 日本語
![](img/lk-miru.gif)
- PDB-8hht: Crystal structure of the SARS-CoV-2 main protease in complex with... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8hht | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the SARS-CoV-2 main protease in complex with Hit-1 | ||||||
![]() | 3C-like proteinase nsp5 | ||||||
![]() | VIRAL PROTEIN / Severe acute respiratory syndrome coronavirus 2 / main protease | ||||||
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 / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / host cell Golgi apparatus / 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 | ![]() ![]() ![]() | ||||||
![]() | Zeng, R. / Xie, L.W. / Huang, C. / Wang, K. / Liu, Y.Z. / Yang, S.Y. / Lei, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: A new generation M pro inhibitor with potent activity against SARS-CoV-2 Omicron variants. Authors: Huang, C. / Shuai, H. / Qiao, J. / Hou, Y. / Zeng, R. / Xia, A. / Xie, L. / Fang, Z. / Li, Y. / Yoon, C. / Huang, Q. / Hu, B. / You, J. / Quan, B. / Zhao, X. / Guo, N. / Zhang, S. / Ma, R. / ...Authors: Huang, C. / Shuai, H. / Qiao, J. / Hou, Y. / Zeng, R. / Xia, A. / Xie, L. / Fang, Z. / Li, Y. / Yoon, C. / Huang, Q. / Hu, B. / You, J. / Quan, B. / Zhao, X. / Guo, N. / Zhang, S. / Ma, R. / Zhang, J. / Wang, Y. / Yang, R. / Zhang, S. / Nan, J. / Xu, H. / Wang, F. / Lei, J. / Chu, H. / Yang, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 79.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 793.2 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hhuC ![]() 7c7pS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
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-LV0 / ~{ | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.24 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.76 Å / Num. obs: 17116 / % possible obs: 87.3 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 3 / Num. unique obs: 1367 / CC1/2: 0.923 / Rpim(I) all: 0.02 / Rrim(I) all: 0.677 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7C7P Resolution: 1.95→34 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.2 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.84 Å2 / Biso mean: 40.1032 Å2 / Biso min: 20.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→34 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
|