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Yorodumi- PDB-7wqj: Crystal structure of MERS main protease in complex with PF07304814 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wqj | ||||||
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Title | Crystal structure of MERS main protease in complex with PF07304814 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / transferase activity / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / membrane => GO:0016020 / single-stranded RNA binding ...host cell membrane / viral genome replication / transferase activity / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / membrane => GO:0016020 / 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 Similarity search - Function | ||||||
Biological species | Middle East respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Lin, C. / Zhang, J. / Li, J. | ||||||
Funding support | 1items
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Citation | Journal: J.Mol.Biol. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wqj.cif.gz | 129.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wqj.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wqj_validation.pdf.gz | 808.1 KB | Display | wwPDB validaton report |
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Full document | 7wqj_full_validation.pdf.gz | 820.3 KB | Display | |
Data in XML | 7wqj_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 7wqj_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/7wqj ftp://data.pdbj.org/pub/pdb/validation_reports/wq/7wqj | HTTPS FTP |
-Related structure data
Related structure data | 7vvpC 7wqhC 7draS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32752.463 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: T2BB45, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase #2: Chemical | ChemComp-80I / [( | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium formate, 0.1M BICINE pH8.5 20% PEG5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979137 Å |
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: 2.75→67.2952 Å / Num. obs: 19794 / % possible obs: 98.5 % / Redundancy: 8.2 % / Biso Wilson estimate: 39.7892961122 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.75→2.9 Å / Rmerge(I) obs: 0.867 / Num. unique obs: 2638 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DRA Resolution: 2.75→67.2952 Å / SU ML: 0.411650301408 / Cross valid method: NONE / σ(F): 1.34653237461 / Phase error: 30.8063880764 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: 39.4799772086 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→67.2952 Å
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Refine LS restraints |
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LS refinement shell |
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