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Yorodumi- PDB-6vl3: The crystal structure of the 2009 H1N1 PA endonuclease mutant I38... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vl3 | ||||||
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Title | The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000986436 | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | VIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Cuypers, M.G. / Slavish, P.J. / Jayaraman, S. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vl3.cif.gz | 57.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vl3.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vl3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6vl3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6vl3_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 6vl3_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/6vl3 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/6vl3 | HTTPS FTP |
-Related structure data
Related structure data | 6v6xC 6v9eC 6vbrC 6vg9C 6vivC 6vjhC 6wijC 6wj4C 7k87C 7lm4C 7lw6C 7m0nC 7mpfC 7mtyC 7n47C 7n55C 7n68C 7n8fC 7rkpC 7umrC 7uuhC 8dipC 8dpjC 8dtwC 8e4sC 5vptS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23136.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1)) Strain: A/Luxembourg/43/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6H0Y9 |
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-Non-polymers , 5 types, 30 molecules
#2: Chemical | #3: Chemical | ChemComp-R1D / | #4: Chemical | ChemComp-QQ4 / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-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: 57.46 % / Description: elongated |
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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: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→45.88 Å / Num. obs: 7558 / % possible obs: 95.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 57.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.015 / Rrim(I) all: 0.03 / Χ2: 0.31 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.68→2.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2 / Num. unique obs: 1001 / CC1/2: 0.889 / Rpim(I) all: 0.177 / Rrim(I) all: 0.35 / Χ2: 0.31 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vpt Resolution: 2.68→33.18 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 141.31 Å2 / Biso mean: 66.6514 Å2 / Biso min: 23.72 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.68→33.18 Å
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LS refinement shell | Resolution: 2.68→2.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 3
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