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- PDB-8ppx: Influenza A/California/07/2009(H1N1) endonuclease in complex with... -

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Basic information

Entry
Database: PDB / ID: 8ppx
TitleInfluenza A/California/07/2009(H1N1) endonuclease in complex with flavonoid-like compound
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / RNA-dependent RNA polymerase / endonuclease inhibitor / flavonoids / antivirals
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
: / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRadilova, K. / Brynda, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: Rsc Med Chem / Year: 2025
Title: Beyond Natural Flavonoids: Exploring Bioisosterism in Design and Synthesis of Influenza Endonuclease Inhibitors
Authors: Reiberger, R. / Kral, M. / Radilova, K. / Kotacka, T. / Tsalyy, A. / Majer, P. / Dracinsky, M. / Brynda, J. / Konvalinka, J. / Kozisek, M. / Machara, A.
History
DepositionJul 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0425
Polymers21,6411
Non-polymers4014
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-20 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.960, 73.960, 128.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 21640.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1))
Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5X6, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 29 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-85W / 5-oxidanyl-2-[4,5,7-tris(oxidanyl)naphthalen-2-yl]-1H-pyrimidin-6-one / 5-oxidanyl-2-[4,5,7-tris(oxidanyl)naphthalen-2-yl]-1~{H}-pyrimidin-6-one


Mass: 286.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10N2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MDP, PEG 1000, PEG 3350, Sodium HEPES, MOPS (acid), Magnesium chloride, Calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 14236 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.271 / Rrim(I) all: 0.278 / Net I/σ(I): 11.93
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.46-2.615.16422890.3215.2931
2.61-2.792.81421530.552.8841
2.79-3.011.52920150.8041.5661
3.01-3.30.86818520.9150.891
3.3-3.680.38816730.9850.3971
3.68-4.250.18414770.9960.1891
4.25-5.190.10512480.9980.1081
5.19-7.30.0979730.9990.11
7.3-100.03955610.0411

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.725 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.602 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25785 385 5 %RANDOM
Rwork0.2265 ---
obs0.22813 7306 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0.52 Å2-0 Å2
2---1.05 Å20 Å2
3---3.39 Å2
Refinement stepCycle: 1 / Resolution: 2.5→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 24 25 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121493
X-RAY DIFFRACTIONr_bond_other_d0.0040.0161329
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.6692013
X-RAY DIFFRACTIONr_angle_other_deg0.3571.5753054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.544510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2110248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0450.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2886.275727
X-RAY DIFFRACTIONr_mcbond_other3.2846.275727
X-RAY DIFFRACTIONr_mcangle_it5.16411.292907
X-RAY DIFFRACTIONr_mcangle_other5.16111.293908
X-RAY DIFFRACTIONr_scbond_it3.4736.449766
X-RAY DIFFRACTIONr_scbond_other3.4716.449766
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.60211.7771107
X-RAY DIFFRACTIONr_long_range_B_refined7.75959.261745
X-RAY DIFFRACTIONr_long_range_B_other7.76259.331746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 28 -
Rwork0.345 527 -
obs--100 %

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