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- PDB-9pn3: Influenza PA-N Endonuclease I38T mutant with compound 4 ((6M)-3-h... -

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Basic information

Entry
Database: PDB / ID: 9pn3
TitleInfluenza PA-N Endonuclease I38T mutant with compound 4 ((6M)-3-hydroxy-4-oxo-6-(2-phenoxyphenyl)-1,4-dihydropyridine-2-carboxylic acid)
ComponentsPolymerase acidic protein
KeywordsLYASE / Metal binding protein / endonuclease / influenza endonuclease
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: 2.36 Å
AuthorsKohlbrand, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI149444 United States
CitationJournal: J.Inorg.Biochem. / Year: 2025
Title: Substituent size versus metal binding of inhibitors with variants of influenza endonuclease.
Authors: Kohlbrand, A.J. / Stokes, R.W. / Sankaran, B. / Cohen, S.M.
History
DepositionJul 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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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)22,8464
Polymers22,4121
Non-polymers4333
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-7 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.357, 75.357, 121.637
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

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Components

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


Mass: 22412.494 Da / Num. of mol.: 1 / Mutation: I38T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-A1CI5 / (6M)-3-hydroxy-4-oxo-6-(2-phenoxyphenyl)-1,4-dihydropyridine-2-carboxylic acid


Mass: 323.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG4000, 100 mM Tris, pH 8.35, 220 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→65.26 Å / Num. obs: 15879 / % possible obs: 100 % / Redundancy: 18.8 % / Biso Wilson estimate: 52.77 Å2 / CC1/2: 1 / Net I/σ(I): 21
Reflection shellResolution: 2.36→2.44 Å / Num. unique obs: 1435 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→65.26 Å / SU ML: 0.2952 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.4944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2792 1590 10.01 %
Rwork0.2233 14289 -
obs0.2289 15879 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.17 Å2
Refinement stepCycle: LAST / Resolution: 2.36→65.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 26 12 1531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781549
X-RAY DIFFRACTIONf_angle_d0.89242078
X-RAY DIFFRACTIONf_chiral_restr0.0504216
X-RAY DIFFRACTIONf_plane_restr0.009266
X-RAY DIFFRACTIONf_dihedral_angle_d17.41583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.440.33361340.33681295X-RAY DIFFRACTION99.79
2.44-2.520.36491480.31771295X-RAY DIFFRACTION99.59
2.52-2.620.28451450.31861296X-RAY DIFFRACTION99.65
2.62-2.740.32931480.28771295X-RAY DIFFRACTION99.65
2.74-2.890.2371470.28751297X-RAY DIFFRACTION99.65
2.89-3.070.31621430.27931291X-RAY DIFFRACTION99.93
3.07-3.310.35441410.27931307X-RAY DIFFRACTION100
3.31-3.640.34171440.22951300X-RAY DIFFRACTION99.93
3.64-4.160.30441440.19091309X-RAY DIFFRACTION100
4.17-5.250.23931540.17721289X-RAY DIFFRACTION100
5.25-65.260.22451420.19231315X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.6962388459 Å / Origin y: 14.6317536566 Å / Origin z: -9.68933734243 Å
111213212223313233
T0.536222580822 Å20.00448043144402 Å20.000892737195429 Å2-0.383652573239 Å20.0377423619565 Å2--0.424141388323 Å2
L3.70999234569 °20.0561554163212 °2-0.473814593624 °2-2.07107883244 °20.0479951244736 °2--1.59466110797 °2
S-0.0167440739946 Å °0.0504080545938 Å °-0.0884380718894 Å °-0.119510405791 Å °0.0166280141462 Å °0.218436149368 Å °-0.0223671178307 Å °-0.0553759258723 Å °-0.00719826469015 Å °
Refinement TLS groupSelection details: all

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