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- PDB-9pnm: Influenza PA-N Endonuclease I38T with compound 3 ((6M)-3-hydroxy-... -

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Basic information

Entry
Database: PDB / ID: 9pnm
TitleInfluenza PA-N Endonuclease I38T 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: 2.14 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 21, 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)22,7224
Polymers22,3341
Non-polymers3873
Water1267
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 area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.194, 75.194, 119.641
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

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Components

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


Mass: 22334.426 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-198)
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.: 7 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
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: 2.14→65.12 Å / Num. obs: 20857 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 58.35 Å2 / CC1/2: 1 / Net I/σ(I): 28
Reflection shellResolution: 2.14→2.2 Å / Num. unique obs: 1438 / CC1/2: 0.892

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→65.12 Å / SU ML: 0.3359 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.5621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2741 2073 9.94 %
Rwork0.225 18784 -
obs0.2299 20857 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.83 Å2
Refinement stepCycle: LAST / Resolution: 2.14→65.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 21 7 1515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361536
X-RAY DIFFRACTIONf_angle_d0.62032060
X-RAY DIFFRACTIONf_chiral_restr0.0406215
X-RAY DIFFRACTIONf_plane_restr0.0051264
X-RAY DIFFRACTIONf_dihedral_angle_d19.6972581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.190.371340.3351222X-RAY DIFFRACTION99.27
2.19-2.240.36211360.29671260X-RAY DIFFRACTION99.86
2.24-2.310.30951360.29081261X-RAY DIFFRACTION100
2.31-2.370.31351370.28941259X-RAY DIFFRACTION99.79
2.37-2.450.29651410.31021234X-RAY DIFFRACTION99.78
2.45-2.540.40411420.3161242X-RAY DIFFRACTION99.78
2.54-2.640.40461360.31441265X-RAY DIFFRACTION99.79
2.64-2.760.28211430.29391257X-RAY DIFFRACTION99.93
2.76-2.90.32941380.26451254X-RAY DIFFRACTION99.86
2.9-3.090.29961410.27521238X-RAY DIFFRACTION99.86
3.09-3.320.32241390.25491257X-RAY DIFFRACTION100
3.32-3.660.27721400.20141244X-RAY DIFFRACTION100
3.66-4.190.26881340.18881274X-RAY DIFFRACTION100
4.19-5.280.20831420.18411244X-RAY DIFFRACTION100
5.28-65.120.24331340.20541273X-RAY DIFFRACTION99.86
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)
17.095799822453.04877395956-1.1772836665.48597171816-1.59797516148.53500398741-0.2192622178960.930542998903-0.818497490032-0.03293648331920.3207250768320.08577216244690.301439794457-0.287639987892-0.2241826941530.65230960401-0.01373039479330.07569576667870.451035674729-0.1830767921550.59834509957829.41023396977.35694218052-20.5645119002
28.029434092020.0884764856991-1.046431663681.90269934311-0.7749251506041.010837288470.0032516141867-0.423370047324-0.6612171461690.1610978059870.004594702903390.193067058343-0.00319669908986-0.07978204651450.006326180523680.709799563873-0.00039003317140.03528745666850.4283207608780.00210867735040.48691908523614.912921958112.7109811756-8.39344231276
36.943926043840.19925984313-0.2282598558671.37522901054-0.8301532532622.087920196190.0641259197572-0.006223657048140.3652701747660.161790002434-0.001827403579640.150506233165-0.0586795686693-0.114654241952-0.04874281491990.665916268426-0.03839820504310.04773065276990.309464564429-0.04063490714660.41967935955727.44528686519.4703827717-5.50471823415
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 31 )-1 - 311 - 33
22chain 'A' and (resid 32 through 126 )32 - 12634 - 108
33chain 'A' and (resid 127 through 198 )127 - 198109 - 180

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