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Yorodumi- PDB-6w5k: 1.95 A resolution structure of Norovirus 3CL protease in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w5k | |||||||||
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Title | 1.95 A resolution structure of Norovirus 3CL protease in complex with inhibitor 5g | |||||||||
Components | 3C-LIKE PROTEASE | |||||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / PROTEASE / Norovirus 3CL protease / Inhibitors / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex | |||||||||
Function / homology | Function and homology information calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Norwalk virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | |||||||||
Authors | Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Rathnayake, A.D. / Kim, Y. / Chang, K.O. / Groutas, W.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Structure-Guided Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. Authors: Rathnayake, A.D. / Kim, Y. / Dampalla, C.S. / Nguyen, H.N. / Jesri, A.M. / Kashipathy, M.M. / Lushington, G.H. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w5k.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w5k.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 6w5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w5k_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6w5k_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6w5k_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 6w5k_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/6w5k ftp://data.pdbj.org/pub/pdb/validation_reports/w5/6w5k | HTTPS FTP |
-Related structure data
Related structure data | 6w5hC 6w5jC 6w5lC 3ur9S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19994.934 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norwalk virus (strain GI/Human/United States/Norwalk/1968) Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q83883, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase #2: Chemical | ChemComp-TKV / #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: 1.87 Å3/Da / Density % sol: 34.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% w/v PEG3350, 0.1M Tris, 200 mM Trimethylamine N-oxide dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→44.71 Å / Num. obs: 42933 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.166 / Net I/σ(I): 7.4 / Num. measured all: 290570 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.988 / Num. measured all: 20460 / Num. unique obs: 3021 / CC1/2: 0.799 / Net I/σ(I) obs: 2.1 / % possible all: 99.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UR9 Resolution: 1.95→37.64 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 32 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.6 Å2 / Biso mean: 33.209 Å2 / Biso min: 10.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→37.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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