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- PDB-9pn2: Influenza PA-N Endonuclease I38T mutant with compound 3 ((6M)-3-h... -

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Basic information

Entry
Database: PDB / ID: 9pn2
TitleInfluenza PA-N Endonuclease I38T mutant with compound 3 ((6M)-3-hydroxy-6-[2-(methylsulfanyl)phenyl]-4-oxo-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: 2.39 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)22,7104
Polymers22,3221
Non-polymers3873
Water59433
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 area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.112, 75.112, 118.972
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-411-

HOH

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Components

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


Mass: 22322.371 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-A1CI4 / (6M)-3-hydroxy-6-[2-(methylsulfanyl)phenyl]-4-oxo-1,4-dihydropyridine-2-carboxylic acid


Mass: 277.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
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: 2.39→65.09 Å / Num. obs: 16274 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 46.71 Å2 / CC1/2: 0.999 / Net I/σ(I): 12
Reflection shellResolution: 2.39→2.58 Å / Num. unique obs: 1609 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→65.05 Å / SU ML: 0.3171 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.0276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2675 1486 9.99 %
Rwork0.2086 13389 -
obs0.2145 14875 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.83 Å2
Refinement stepCycle: LAST / Resolution: 2.39→65.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 21 33 1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231522
X-RAY DIFFRACTIONf_angle_d0.43942042
X-RAY DIFFRACTIONf_chiral_restr0.0379214
X-RAY DIFFRACTIONf_plane_restr0.004261
X-RAY DIFFRACTIONf_dihedral_angle_d18.2021575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.470.28231380.28171225X-RAY DIFFRACTION99.78
2.47-2.560.35131310.2851206X-RAY DIFFRACTION99.41
2.56-2.660.30991380.27971225X-RAY DIFFRACTION99.93
2.66-2.780.29941310.2661206X-RAY DIFFRACTION99.93
2.78-2.930.33461410.26311209X-RAY DIFFRACTION99.85
2.93-3.110.32181330.26661220X-RAY DIFFRACTION99.78
3.11-3.350.33881360.23581220X-RAY DIFFRACTION100
3.35-3.690.28771340.19381213X-RAY DIFFRACTION100
3.69-4.220.27471350.17471216X-RAY DIFFRACTION100
4.22-5.30.21711350.16661214X-RAY DIFFRACTION99.85
5.32-65.050.20331340.19311235X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.181323144176.402071968690.9946968316185.72867017674-1.551356899729.53879263515-0.2605987274530.928091355872-0.433381757754-0.00645561176140.4071395827690.381570447184-0.0189066554575-0.22608989144-0.09940183401410.5794152502430.1162787932470.1246998971430.430229530931-0.171138360020.58263323281129.14092998417.38922774199-20.357586843
27.805060583420.636984692672-0.321514483031.717651335410.1751689017011.969585921640.101371896357-0.261706487154-0.370799344140.0706141259441-0.07439963480750.0249084278611-0.00184208573728-0.305149837325-0.04440332047270.4565757771760.02715414274280.09102368321130.355332273163-0.01737306932380.37914069644814.829221844412.5018297659-8.22069552514
34.574430133091.313663263180.0659167345538.18173016977-6.030785451935.693715500370.183105586093-0.08531770237971.13890614728-0.2782407400880.119996307730.123822918005-0.335144077192-0.189161239546-0.2831543274530.5592254847550.02465366398240.06156909131820.306992383694-0.08838077810180.51725264880218.800934992825.1320967829-6.45528899285
47.85058406806-1.72774567335-2.855727991751.416808181491.079440870965.516779127930.00440954261983-0.401011791322-0.116471434120.03207194164380.006401336660970.0232012670026-0.06275085714670.206259211557-0.05806728628390.453472016754-0.03405264652990.02783795822360.231697775648-0.01387232699690.32227444321131.358266781316.4237402933-4.67609026555
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 31 )A-1 - 311 - 33
22chain 'A' and (resid 32 through 126 )A32 - 12634 - 108
33chain 'A' and (resid 127 through 149 )A127 - 149109 - 131
44chain 'A' and (resid 150 through 198 )A - C150 - 302132

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