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- PDB-8t6z: Influenza PAN endonuclease I38T mutant with 6-(4-(1H-tetrazol-5-y... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t6z | ||||||
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Title | Influenza PAN endonuclease I38T mutant with 6-(4-(1H-tetrazol-5-yl)-2-(trifluoromethyl)phenyl)-3-hydroxy-4-oxo-1,4-dihydropyridine-2-carboxylic acid | ||||||
![]() | Polymerase acidic protein | ||||||
![]() | VIRAL PROTEIN / HYDROLASE/INHIBITOR / Influenza endonuclease / resistance / drug discovery / metal-binding pharmacophore / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kohlbrand, A.J. / Cohen, S.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Studies of Inhibitors with Clinically Relevant Influenza Endonuclease Variants. Authors: Kohlbrand, A.J. / Stokes, R.W. / Sankaran, B. / Cohen, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.8 KB | Display | ![]() |
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PDB format | ![]() | 69 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 767.5 KB | Display | ![]() |
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Full document | ![]() | 770.6 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t5wC ![]() 8t5zC ![]() 8t67C ![]() 8t81C ![]() 8t94C ![]() 8vgzC ![]() 8t5v C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22412.494 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: I38T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds | ||||||
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#2: Chemical | #3: Chemical | ChemComp-IJM / ( | Mass: 367.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8F3N5O4 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 306 K / Method: vapor diffusion, hanging drop Details: 32% PEG (MW 4000 g/mol), 100 mM Tris (pH 8.35), and 220 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→65.78 Å / Num. obs: 27414 / % possible obs: 100 % / Redundancy: 30.8 % / Biso Wilson estimate: 47.19 Å2 / CC1/2: 1 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.91→1.98 Å / Num. unique obs: 1620 / CC1/2: 0.425 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 63.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→65.74 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 |
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