[English] 日本語
Yorodumi- PDB-8dd6: SARS-CoV-2 Main Protease (Mpro) H163A Mutant in Complex with GC376 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dd6 | ||||||
---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 Main Protease (Mpro) H163A Mutant in Complex with GC376 | ||||||
Components | ORF1a polyprotein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / cysteine protease / SARS-CoV-2 / 3CL-like / GC376 / VIRAL PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated suppression of host gene expression / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated suppression of host gene expression / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tran, N. / McLeod, M.J. / Kalyaanamoorthy, S. / Ganesan, A. / Holyoak, T. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2023 Title: The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Authors: Tran, N. / Dasari, S. / Barwell, S.A.E. / McLeod, M.J. / Kalyaanamoorthy, S. / Holyoak, T. / Ganesan, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8dd6.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8dd6.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 8dd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dd6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8dd6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8dd6_validation.xml.gz | 14 KB | Display | |
Data in CIF | 8dd6_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/8dd6 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/8dd6 | HTTPS FTP |
-Related structure data
Related structure data | 8ddlC 8sg6C 7alhS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 33758.477 Da / Num. of mol.: 1 / Mutation: H163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U3EDN3 |
---|---|
#2: Chemical | ChemComp-DMS / |
#3: Chemical | ChemComp-K36 / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.7 % / Description: Thin plates in a "flower" arrangement |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris, pH 6.5, 25% (w/v) PEG 3350, and 3% (v/v) DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.1271 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→54.99 Å / Num. obs: 11561 / % possible obs: 99.96 % / Redundancy: 6.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.075 / Rrim(I) all: 0.191 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 6.72 % / Rmerge(I) obs: 0.895 / Num. unique obs: 558 / CC1/2: 0.814 / Rpim(I) all: 0.374 / Rrim(I) all: 0.971 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ALH Resolution: 2.3→54.97 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / Phase error: 25.88 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→54.97 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|