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- PDB-8dhn: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -

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Basic information

Entry
Database: PDB / ID: 8dhn
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 6-Bromo-3-hydroxy-2-(5-methyl-1,2,4-oxadiazol-3-yl)pyridin-4(1H)-one
ComponentsPA endonuclease
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / Drug discovery / metal-binding pharmacophore / isosteres / influenza endonuclease / VIRAL PROTEIN-INHIBITOR complex / ANTIVIRAL PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology: / Chem-T6U
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKohlbrand, A.J. / Stokes, R.W. / Karges, J. / Seo, H. / Sankaran, B. / Cohen, S.M.
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: Acs Med.Chem.Lett. / Year: 2023
Title: Carboxylic Acid Isostere Derivatives of Hydroxypyridinones as Core Scaffolds for Influenza Endonuclease Inhibitors.
Authors: Stokes, R.W. / Kohlbrand, A.J. / Seo, H. / Sankaran, B. / Karges, J. / Cohen, S.M.
History
DepositionJun 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PA endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8064
Polymers22,4251
Non-polymers3823
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.034, 75.034, 121.240
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-333-

HOH

21A-366-

HOH

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Components

#1: Protein PA endonuclease


Mass: 22424.547 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009(H1N1) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-T6U / (2P)-6-bromo-3-hydroxy-2-(5-methyl-1,2,4-oxadiazol-3-yl)pyridin-4(1H)-one


Mass: 272.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6BrN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→65.01 Å / Num. obs: 15004 / % possible obs: 99.9 % / Redundancy: 29 % / Biso Wilson estimate: 47.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.102 / Net I/σ(I): 20
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 1.439 / Mean I/σ(I) obs: 2 / Num. unique obs: 806 / CC1/2: 0.84 / Rpim(I) all: 0.33

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
APEX 2data reduction
APEX 2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6V

6e6v


Resolution: 2.4→64.98 Å / SU ML: 0.2803 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.7585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 1509 10.06 %
Rwork0.2006 13495 -
obs0.2062 15004 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→64.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 17 83 1566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421515
X-RAY DIFFRACTIONf_angle_d0.62012034
X-RAY DIFFRACTIONf_chiral_restr0.0406215
X-RAY DIFFRACTIONf_plane_restr0.0028258
X-RAY DIFFRACTIONf_dihedral_angle_d19.2003569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.32051360.27921221X-RAY DIFFRACTION98.69
2.47-2.560.32671360.26641216X-RAY DIFFRACTION99.85
2.56-2.660.36061400.26831227X-RAY DIFFRACTION99.85
2.66-2.790.36051380.26971230X-RAY DIFFRACTION100
2.79-2.930.34131350.26451222X-RAY DIFFRACTION100
2.93-3.120.3041400.24931242X-RAY DIFFRACTION99.78
3.12-3.360.24581350.21681205X-RAY DIFFRACTION99.93
3.36-3.690.2571360.18081237X-RAY DIFFRACTION99.78
3.69-4.230.23331300.15341243X-RAY DIFFRACTION99.93
4.23-5.320.19291370.16031225X-RAY DIFFRACTION100
5.33-64.980.2381460.19731227X-RAY DIFFRACTION99.71
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)
16.023294867812.261696325292.436567333618.58770793418-2.546245044055.305689825940.161026571290.871086084337-0.372805103623-0.3585816409520.08792558464040.2380589006480.6508126658430.299078254156-0.330513152610.51920841350.04712018209280.06084496600140.438887564336-0.1609834562980.46993445934929.41759822137.16560145095-20.4442739647
24.306934609460.469266222652-0.2769765182411.82976901467-0.4404955269852.360677192730.120081509256-0.438276462678-0.2188942014130.0386171991768-0.05980560704330.3839770256270.0188941963627-0.215482378774-0.01274312170680.4193740977710.003389247198470.0299644783370.3484172914820.00968455782420.45061723215515.05745369812.8974705746-8.60511127276
37.97726225626-2.049534197060.5033057128943.99014747214-0.3642163053352.442105719950.156837285267-0.2531001181970.0975916203860.0447626126003-0.03436123838730.261539606652-0.082621759815-0.080406243342-0.1293193680220.373516419841-0.0228474234681-0.01088557074140.211833576605-0.02180632125560.24704405855427.25941421919.611309213-5.71907303199
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 31 )-1 - 312 - 34
22chain 'A' and (resid 32 through 126 )32 - 12635 - 108
33chain 'A' and (resid 127 through 198 )127 - 198109 - 180

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