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Yorodumi- PDB-7d3c: The newly emerged SARS-like coronavirus HCoV-EMC also has an "Ach... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d3c | |||||||||
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Title | The newly emerged SARS-like coronavirus HCoV-EMC also has an "Achilles' heel": current effective inhibitor targeting a 3C-like protease | |||||||||
Components |
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Keywords | VIRAL PROTEIN / MERS-CoV / Nsp5 / N3 | |||||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / SARS coronavirus main proteinase / transferase activity / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / membrane => GO:0016020 ...host cell membrane / viral genome replication / SARS coronavirus main proteinase / transferase activity / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / 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 / zinc ion binding Similarity search - Function | |||||||||
Biological species | Middle East respiratory syndrome-related coronavirus synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Yan, L. / Ren, Z. | |||||||||
Citation | Journal: Protein cell / Year: 2013 Title: The newly emerged SARS-like coronavirus HCoV-EMC also has an "Achilles' heel": current effective inhibitor targeting a 3C-like protease Authors: Ren, Z. / Yan, L. / Zhang, N. / Guo, Y. / Yang, C. / Lou, Z. / Rao, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d3c.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d3c.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 7d3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d3c_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 7d3c_full_validation.pdf.gz | 482.2 KB | Display | |
Data in XML | 7d3c_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 7d3c_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/7d3c ftp://data.pdbj.org/pub/pdb/validation_reports/d3/7d3c | HTTPS FTP |
-Related structure data
Related structure data | 1uj1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33355.160 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(DE3) (bacteria) References: UniProt: A0A0D3MU45, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase #2: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 680.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) References: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE #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: 2.81 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 200 mM Trimethylamine N-oxide dihydrate, 0.02 M cadmium chloride hydrate, 100 mM Tris-HCl (pH 8.5), and 16% w/v polyethylene glycol monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 240588 / % possible obs: 100 % / Redundancy: 5.67 % / CC1/2: 0.8 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.2→2.3 Å / Num. unique obs: 5134 / CC1/2: 0.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UJ1 Resolution: 2.2→32.222 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.488 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.13 Å2 / Biso mean: 37.28 Å2 / Biso min: 16.38 Å2
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Refinement step | Cycle: final / Resolution: 2.2→32.222 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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