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Yorodumi- PDB-4m9t: NS2B-NS3 protease from dengue virus in the presence of DTNB, a co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m9t | ||||||
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Title | NS2B-NS3 protease from dengue virus in the presence of DTNB, a covalent allosteric inhibitor | ||||||
Components | NS2B-NS3 protease | ||||||
Keywords | VIRAL PROTEIN / serine protease / allosteric inhibition / dengue virus protease / trypsin-like protease / conformational flexibility | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Bell, J.A. / Yildiz, M. / Hardy, J.A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Allosteric Inhibition of the NS2B-NS3 Protease from Dengue Virus. Authors: Yildiz, M. / Ghosh, S. / Bell, J.A. / Sherman, W. / Hardy, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m9t.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m9t.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 4m9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/4m9t ftp://data.pdbj.org/pub/pdb/validation_reports/m9/4m9t | HTTPS FTP |
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-Related structure data
Related structure data | 4m9fC 4m9iC 4m9kC 4m9mC 2fomS 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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Unit cell |
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-Components
#1: Protein | Mass: 26360.479 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1394-1440, 1476-1660 / Mutation: A125C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 / Gene: NS2B-NS3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q91H74, UniProt: P12823*PLUS |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Sequence details | THIS PROTEIN IS A FUSION PROTEIN CONTAINING RESIDUES 43-95 FROM DENGUE VIRUS NS2B, A GGGGSGGGG ...THIS PROTEIN IS A FUSION PROTEIN CONTAINING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 40% PEG200, 0.1 M Acetic acid, pH 5.5. Crystals were soaked in 40% PEG200, 0.1 M Tris pH 8.5, 5 mM 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2012 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→43.7 Å / Num. all: 19456 / Num. obs: 19455 / % possible obs: 85.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 30.1 |
Reflection shell | Highest resolution: 1.7 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 1.85 / Num. unique all: 19456 / Rsym value: 0.114 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FOM Resolution: 1.74→43.66 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 10000 / σ(I): 10000 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: This structure was solved in the presence of the small-molecule NS2B-NS3pro inhibitor DTNB, however density for DTNB could not be observed in the structure.
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Solvent computation | Bsol: 48.0016 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.97 Å2 / Biso mean: 28.8415 Å2 / Biso min: 4.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→43.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
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