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Yorodumi- PDB-5dgj: 1.0A resolution structure of Norovirus 3CL protease in complex an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dgj | ||||||
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Title | 1.0A resolution structure of Norovirus 3CL protease in complex an oxadiazole-based, cell permeable macrocyclic (20-mer) inhibitor | ||||||
Components | 3C-LIKE PROTEASE | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / PROTEASE / NOROVIRUS / NORWALK VIRUS / ANTIVIRAL INHIBITORS / OXADIAZOLE INHIBITOR / CELL PERMEABLE / 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 / Resolution: 1 Å | ||||||
Authors | Lovell, S. / Battaile, K.P. / Mehzabeen, N. / Damalanka, V.C. / Kim, Y. / Alliston, K.R. / Weerawarna, P.M. / Kankanamalage, A.C.G. / Lushington, G.H. / Chang, K.-O. / Groutas, W.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: Oxadiazole-Based Cell Permeable Macrocyclic Transition State Inhibitors of Norovirus 3CL Protease. Authors: Damalanka, V.C. / Kim, Y. / Alliston, K.R. / Weerawarna, P.M. / Galasiti Kankanamalage, A.C. / Lushington, G.H. / Mehzabeen, N. / 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 | 5dgj.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dgj.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 5dgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dgj_validation.pdf.gz | 833.9 KB | Display | wwPDB validaton report |
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Full document | 5dgj_full_validation.pdf.gz | 835.2 KB | Display | |
Data in XML | 5dgj_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 5dgj_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/5dgj ftp://data.pdbj.org/pub/pdb/validation_reports/dg/5dgj | HTTPS FTP |
-Related structure data
Related structure data | 5dg6C 3ur9S C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20126.131 Da / Num. of mol.: 1 / Fragment: UNP residues 1101-1281 Source method: isolated from a genetically manipulated source Details: N-terminal hexahistidine tag / Source: (gene. exp.) Norwalk virus / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q83883, calicivirin |
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#2: Chemical | ChemComp-V64 / Type: Peptide-like / Class: Inhibitor / Mass: 592.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H48N6O7 References: tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-22-oxa-6,9,14,20,21-pentaazabicyclo[17.2.1]docosa-1(21),19-dien-4-yl]carbamate |
#3: 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: 1.94 Å3/Da / Density % sol: 36.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH), 0.05 M BIS-TRIS, 0.05 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1→34.21 Å / Num. obs: 82788 / % possible obs: 99.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 10.74 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.1 / Num. measured all: 261523 / Scaling rejects: 132 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UR9 Resolution: 1→32.202 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 13.64 / 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: 52.95 Å2 / Biso mean: 17.1397 Å2 / Biso min: 6.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1→32.202 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28
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