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Yorodumi- PDB-5ko3: Structure of a Core Papain-like Protease of MERS Coronavirus with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ko3 | ||||||||||||
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Title | Structure of a Core Papain-like Protease of MERS Coronavirus with utility for structure-based drug design | ||||||||||||
Components | ORF1a | ||||||||||||
Keywords | HYDROLASE / MERS PLpro / substrate-binding loop | ||||||||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / transferase activity / symbiont-mediated degradation of host mRNA ...host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / transferase activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||||||||
Biological species | Middle East respiratory syndrome coronavirus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å | ||||||||||||
Authors | Clasman, J.C. / Baez-Santos, Y.M. / Mesecar, A.D. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Sci Rep / Year: 2017 Title: X-ray Structure and Enzymatic Activity Profile of a Core Papain-like Protease of MERS Coronavirus with utility for structure-based drug design. Authors: Clasman, J.R. / Baez-Santos, Y.M. / Mettelman, R.C. / O'Brien, A. / Baker, S.C. / 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 | 5ko3.cif.gz | 70.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ko3.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ko3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/5ko3 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5ko3 | HTTPS FTP |
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-Related structure data
Related structure data | 4p16S 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: 28730.473 Da / Num. of mol.: 1 / Fragment: Peptidase C16 residues 1544-1800 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome coronavirus Production host: Escherichia coli (E. coli) / References: UniProt: A0A023J538, UniProt: K9N7C7*PLUS | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 5.5 M Ammonium acetate, vapor diffusion, sitting drop, 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.949→100 Å / Num. obs: 29405 / % possible obs: 98.8 % / Redundancy: 4.1 % / Net I/σ(I): 26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P16 Resolution: 1.949→43.205 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.949→43.205 Å
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Refine LS restraints |
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LS refinement shell |
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