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Yorodumi- PDB-8ddb: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ddb | ||||||
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Title | The N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 4-(benzyloxy)-6-bromo-3-hydroxypicolinic acid | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / Drug discovery / metal-binding pharmacophore / isosteres / influenza endonuclease / HYDROLASE-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 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: 2.15 Å | ||||||
Authors | Kohlbrand, A.J. / Stokes, R.W. / Karges, J. / Seo, H. / Sankaran, B. / Cohen, S.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2023 Title: Carboxylic Acid Isostere Derivatives of Hydroxypyridinones as Core Scaffolds for Influenza Endonuclease Inhibitors. Authors: Stokes, R.W. / Kohlbrand, A.J. / Seo, H. / Sankaran, B. / Karges, J. / Cohen, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ddb.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ddb.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ddb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ddb_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
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Full document | 8ddb_full_validation.pdf.gz | 473.5 KB | Display | |
Data in XML | 8ddb_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 8ddb_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/8ddb ftp://data.pdbj.org/pub/pdb/validation_reports/dd/8ddb | HTTPS FTP |
-Related structure data
Related structure data | 7v04C 8ctfC 8dalC 8ddeC 8dhnC 8djvC 8djyC 6e6vS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22367.428 Da / Num. of mol.: 1 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1)) Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli BL21 (bacteria) References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds |
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-Non-polymers , 5 types, 85 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-R6X / | #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: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 32% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→66.05 Å / Num. obs: 21524 / % possible obs: 100 % / Redundancy: 25 % / Biso Wilson estimate: 53.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.015 / Rrim(I) all: 0.071 / Net I/av σ(I): 25.6 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 1.288 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1158 / CC1/2: 0.876 / Rpim(I) all: 0.4 / Rrim(I) all: 1.314 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6E6V Resolution: 2.15→58.02 Å / SU ML: 0.284 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.424 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: 70.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→58.02 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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