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Yorodumi- PDB-5e0g: 1.20 A resolution structure of Norovirus 3CL protease in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e0g | ||||||
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Title | 1.20 A resolution structure of Norovirus 3CL protease in complex with a triazole-based macrocyclic (17-mer) inhibitor | ||||||
Components | Norovirus 3C-like protease | ||||||
Keywords | PROTEASE/PROTEASE INHIBITOR / protease / norovirus / norwalk virus / antiviral inhibitors / triazole macrocyclic inhibitor / cell permeable / PROTEASE-PROTEASE INHIBITOR complex | ||||||
Function / homology | Function and homology information calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication ...calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Norwalk virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Lovell, S. / Battaile, K.P. / Mehzabeen, N. / Weerawarna, P.M. / Kim, Y. / Kankanamalage, A.C.G. / Damalanka, V.C. / Lushington, G.H. / Alliston, K.R. / Chang, K.-O. / Groutas, W.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2016 Title: Structure-based design and synthesis of triazole-based macrocyclic inhibitors of norovirus protease: Structural, biochemical, spectroscopic, and antiviral studies. Authors: Weerawarna, P.M. / Kim, Y. / Galasiti Kankanamalage, A.C. / Damalanka, V.C. / Lushington, G.H. / Alliston, K.R. / 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 | 5e0g.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e0g.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 5e0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e0g_validation.pdf.gz | 819.1 KB | Display | wwPDB validaton report |
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Full document | 5e0g_full_validation.pdf.gz | 819.9 KB | Display | |
Data in XML | 5e0g_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 5e0g_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/5e0g ftp://data.pdbj.org/pub/pdb/validation_reports/e0/5e0g | HTTPS FTP |
-Related structure data
Related structure data | 5e0hC 5e0jC 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 Source: (gene. exp.) Norwalk virus / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q83883, calicivirin |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-5LG / ( Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 543.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H37N7O6 References: (phenylmethyl) ~{N}-[(8~{S},11~{S},14~{S})-8-(hydroxymethyl)-11-(2-methylpropyl)-5,10,13-tris(oxidanylidene)-1,4,9,12,17,18-hexazabicyclo[14.2.1]nonadeca-16(19),17-dien-14-yl]carbamate |
#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: 1.87 Å3/Da / Density % sol: 34.07 % / Description: prism |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG2000 MME, 150 mM potassium bromide |
-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 | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.2→33.24 Å / Num. obs: 44826 / % possible obs: 96.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.1 / Num. measured all: 147835 / Scaling rejects: 2 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.2 % / Rejects: _
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-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: PDB entry 3UR9 Resolution: 1.2→31.178 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 15.25 / 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: 62.62 Å2 / Biso mean: 20.2539 Å2 / Biso min: 7.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→31.178 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: 16
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