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- PDB-5jun: PB2 bound to an azaindole inhibitor -

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Basic information

Entry
Database: PDB / ID: 5jun
TitlePB2 bound to an azaindole inhibitor
ComponentsPolymerase basic protein 2
KeywordsRNA BINDING PROTEIN / flu / polymerase / nucleotide binding / inhibitor
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / : / Influenza RNA polymerase PB2 helical domain / Influenza RNA polymerase PB2 CAP binding domain
Similarity search - Domain/homology
Chem-6NU / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.69 Å
AuthorsJacobs, M.D.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Discovery of Novel, Orally Bioavailable beta-Amino Acid Azaindole Inhibitors of Influenza PB2.
Authors: Farmer, L.J. / Clark, M.P. / Boyd, M.J. / Perola, E. / Jones, S.M. / Tsai, A. / Jacobs, M.D. / Bandarage, U.K. / Ledeboer, M.W. / Wang, T. / Deng, H. / Ledford, B. / Gu, W. / Duffy, J.P. / ...Authors: Farmer, L.J. / Clark, M.P. / Boyd, M.J. / Perola, E. / Jones, S.M. / Tsai, A. / Jacobs, M.D. / Bandarage, U.K. / Ledeboer, M.W. / Wang, T. / Deng, H. / Ledford, B. / Gu, W. / Duffy, J.P. / Bethiel, R.S. / Shannon, D. / Byrn, R.A. / Leeman, J.R. / Rijnbrand, R. / Bennett, H.B. / O'Brien, C. / Memmott, C. / Nti-Addae, K. / Bennani, Y.L. / Charifson, P.S.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5622
Polymers19,1741
Non-polymers3871
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.360, 81.360, 54.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 19174.324 Da / Num. of mol.: 1
Fragment: Influenza RNA-dependent RNA polymerase subunit PB2
Source method: isolated from a genetically manipulated source
Details: artifact / Source: (gene. exp.) Influenza A virus / Strain: A/Beijing/39/1975 H3N2 / Gene: PB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q30NP1
#2: Chemical ChemComp-6NU / (3~{R})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]-3-(1-methylcyclobutyl)propanoic acid


Mass: 387.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19F2N5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well ...Details: 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well solution (1.5 M sodium formate, 100 mM sodium citrate, pH 4.7, 10 mM dithiothreitol) suspended over 1 mL of well solution, crystals transferred to a soaking solution (3.25 M sodium formate, 100 mM sodium citrate, pH 4.7) containing 1 mM inhibitor, incubated approximately 15 hours at room temperature, and then transferred to a cryo-preservative solution (soaking solution with 25% v/v glycerol) prior to freezing in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.598→29.64 Å / Num. obs: 6190 / % possible obs: 95.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 69.46 Å2 / Rsym value: 0.052 / Net I/av σ(I): 14.2 / Net I/σ(I): 23.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.6-2.744.70.5451.4199.9
2.74-2.950.322.4199.9
2.9-3.150.1834.21100
3.1-3.3550.1077.11100
3.35-3.674.90.05314.1179.7
3.67-4.114.90.03720.4178.1
4.11-4.7450.02528.3199.8
4.74-5.814.90.02430.1199.8
5.81-8.214.90.02134.2199.7
8.21-25.5494.70.01345196.4

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
BUSTER-TNT2.11.6refinement
PDB_EXTRACT3.2data extraction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4NCE

4nce


Resolution: 2.69→29.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.824 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.249
RfactorNum. reflection% reflectionSelection details
Rfree0.189 276 4.97 %RANDOM
Rwork0.176 ---
obs0.176 5549 95 %-
Displacement parametersBiso max: 180.75 Å2 / Biso mean: 64.59 Å2 / Biso min: 23.69 Å2
Baniso -1Baniso -2Baniso -3
1--3.8039 Å20 Å20 Å2
2---3.8039 Å20 Å2
3---7.6077 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.69→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 28 17 1299
Biso mean--45.76 52.16 -
Num. residues----160
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d484SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes214HARMONIC5
X-RAY DIFFRACTIONt_it1306HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion170SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1475SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1306HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1755HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion20.27
LS refinement shellResolution: 2.69→3.01 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.221 89 5.39 %
Rwork0.202 1561 -
all-1650 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -37.9523 Å / Origin y: -0.3006 Å / Origin z: 2.7032 Å
111213212223313233
T-0.0076 Å20.0611 Å2-0.0065 Å2--0.2264 Å2-0.0043 Å2---0.2207 Å2
L1.802 °20.704 °21.1992 °2-8.8444 °23.7882 °2--4.8236 °2
S-0.1834 Å °0.2023 Å °-0.0101 Å °-0.7997 Å °0.1672 Å °0.0653 Å °-0.4802 Å °0.2323 Å °0.0161 Å °
Refinement TLS groupSelection details: { A|* }

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