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Yorodumi- PDB-2fp7: West Nile Virus NS2B/NS3protease in complex with Bz-Nle-Lys-Arg-Arg-H -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fp7 | |||||||||
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Title | West Nile Virus NS2B/NS3protease in complex with Bz-Nle-Lys-Arg-Arg-H | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Flavivirus / NS3 protease / NS2B cofactor / substrate-based inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / positive regulation of viral genome replication ...RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / positive regulation of viral genome replication / 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 / protein-DNA complex / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / peptidase activity / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | West Nile virus synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Schiering, N. / D'Arcy, A. / Erbel, P. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus. Authors: Erbel, P. / Schiering, N. / D'Arcy, A. / Renatus, M. / Kroemer, M. / Lim, S.P. / Yin, Z. / Keller, T.H. / Vasudevan, S.G. / Hommel, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fp7.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fp7.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 2fp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/2fp7 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/2fp7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 6101.576 Da / Num. of mol.: 1 / Fragment: NS2b Source method: isolated from a genetically manipulated source Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P06935, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase |
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#2: Protein | Mass: 18588.094 Da / Num. of mol.: 1 / Fragment: NS3pro Source method: isolated from a genetically manipulated source Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P06935, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase |
#3: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 663.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) References: N-benzoyl-L-norleucyl-6-ammonio-L-norleucyl-N~5~-[amino(iminio)methyl]-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-ornithinamide |
#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: 2.42 Å3/Da / Density % sol: 49.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 Details: 2 M ammonioum sulfate, 100mM HEPES., pH 8.5, VAPOR DIFFUSION, temperature 321K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00005 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→81 Å / Num. all: 26547 / Num. obs: 26547 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.68→1.73 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.313 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse - obtained by SAD phasing Resolution: 1.68→46.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.533 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→46.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.724 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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