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Yorodumi- PDB-6w81: Structure of PEDV main protease bound to potent broad-spectrum no... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w81 | ||||||
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Title | Structure of PEDV main protease bound to potent broad-spectrum non-covalent inhibitor X77 | ||||||
Components | Peptidase C30 | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / COVID-19 / porcine epidemic diarrhea virus / PEDV / main protease / 3C-like protease / 3CL protease / 3Clpro / Mpro / broad-spectrum / inhibitor / proteinase / non-covalent / reversible / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / ANTIVIRAL PROTEIN / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information RNA exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / viral genome replication / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification ...RNA exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / viral genome replication / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / cysteine-type deubiquitinase activity / membrane => GO:0016020 / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Porcine epidemic diarrhea virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Mesecar, A.D. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19) Authors: Mesecar, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w81.cif.gz | 310.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w81.ent.gz | 210.5 KB | Display | PDB format |
PDBx/mmJSON format | 6w81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w81_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6w81_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6w81_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 6w81_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/6w81 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/6w81 | HTTPS FTP |
-Related structure data
Related structure data | 6w63C 6w79C 6wcoC 5hyoS S: Starting model for refinement C: citing same article (ref.) |
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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: 32820.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine epidemic diarrhea virus / Gene: ORF1ab / Production host: Escherichia coli (E. coli) / References: UniProt: S0AP56 #2: Chemical | #3: Chemical | ChemComp-MLA / | #4: 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: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEDV-3CLpro:77 inhibitor complex was co-crystallized by setting up 2 uL drops that were composed of 1 uL of purified PEDV-3CLpro (2.4 mg/mL) that had been incubated for three hours with a 3 ...Details: PEDV-3CLpro:77 inhibitor complex was co-crystallized by setting up 2 uL drops that were composed of 1 uL of purified PEDV-3CLpro (2.4 mg/mL) that had been incubated for three hours with a 3 molar excess of compound 77, and 1 uL of reservoir solution: 0.20 M malonic acid (MIB) pH 4.0 and 25% PEG-3350 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Dry nitrogen stream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.988 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 76919 / % possible obs: 97.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 20.34 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.086 / Χ2: 1.9 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 3111 / CC1/2: 0.637 / CC star: 0.882 / Rpim(I) all: 0.469 / Χ2: 0.849 / % possible all: 79.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HYO Resolution: 1.55→27.87 Å / SU ML: 0.2102 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.366
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→27.87 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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