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Yorodumi- PDB-7rkp: The crystal structure of I38T mutant PA endonuclease (2009/H1N1/C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rkp | ||||||
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Title | The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with cyclic compound SJ001034733 | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | Viral Protein / Hydrolase / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / VIRAL PROTEIN-Inhibitor complex | ||||||
Function / homology | Function and homology information cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Cuypers, M.G. / Slavish, J.P. / Rankovic, Z. / White, S.W. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2023 Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential. Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W. #1: Journal: Eur.J.Med.Chem. / Year: 2023 Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential. Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rkp.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rkp.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 7rkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rkp_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7rkp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7rkp_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 7rkp_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/7rkp ftp://data.pdbj.org/pub/pdb/validation_reports/rk/7rkp | HTTPS FTP |
-Related structure data
Related structure data | 6v6xC 6v9eC 6vbrC 6vg9C 6vivC 6vjhC 6vl3C 6wijC 6wj4C 7k87C 7lm4C 7lw6C 7m0nC 7mpfC 7mtyC 7n47C 7n55C 7n68C 7n8fC 7umrC 7uuhC 8dipC 8dpjC 8dtwC 8e4sC 5vptS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1) Strain: swl A/California/04/2009 H1N1 / Cell line: 2009 / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds |
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-Non-polymers , 5 types, 12 molecules
#2: Chemical | ChemComp-QQ4 / | ||||
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#3: Chemical | ChemComp-5Y1 / ( | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 10 MM MNCL2, 10 MM MGCL2, 0.5% PVP K15 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→74.39 Å / Num. obs: 11501 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.02 / Χ2: 0.65 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.36→2.45 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1162 / CC1/2: 0.853 / Rpim(I) all: 0.378 / Χ2: 0.65 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vpt Resolution: 2.36→45.92 Å / SU ML: 0.3304 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3684 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: 72.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→45.92 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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