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Yorodumi- PDB-7pfy: Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pfy | ||||||
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Title | Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2241 | ||||||
Components |
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Keywords | VIRAL PROTEIN / FLAVIVIRIN / SERINE PROTEASE / NS2B-NS3 / ZIKA VIRUS | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization 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 / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Zika virus synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Huber, S. / Heine, A. / Steinmetzer, T. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Structure-Based Optimization and Characterization of Macrocyclic Zika Virus NS2B-NS3 Protease Inhibitors. Authors: Huber, S. / Braun, N.J. / Schmacke, L.C. / Quek, J.P. / Murra, R. / Bender, D. / Hildt, E. / Luo, D. / Heine, A. / Steinmetzer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pfy.cif.gz | 156.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pfy.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 7pfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pfy_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 7pfy_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | 7pfy_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 7pfy_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/7pfy ftp://data.pdbj.org/pub/pdb/validation_reports/pf/7pfy | HTTPS FTP |
-Related structure data
Related structure data | 7o2mC 7o55C 7obvC 7oc2C 7pfqC 7pfzC 7pg1C 7pgcC 7vlgC 7vlhC 7vliC 5gpiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 5865.384 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Plasmid: bZiPro / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q32ZE1 |
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#2: Protein | Mass: 19037.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Plasmid: bZiPro / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase |
#3: Protein/peptide | Mass: 673.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate 0.2 M ammonium sulfate 20% PEG2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→47.27 Å / Num. obs: 49636 / % possible obs: 99 % / Redundancy: 4.81 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.995 / Rsym value: 0.071 / Net I/σ(I): 11.59 |
Reflection shell | Resolution: 1.38→1.46 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 7523 / CC1/2: 0.911 / Rsym value: 0.376 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GPI Resolution: 1.38→37.34 Å / SU ML: 0.1267 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.9052 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 25.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→37.34 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -6.16631587268 Å / Origin y: -16.9424146119 Å / Origin z: 11.3630139032 Å
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Refinement TLS group | Selection details: all |