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- PDB-6nel: 4-(2-(4-fluorophenyl)-5-hydroxy-6-oxo-1,6-dihydropyridin-3-yl)ben... -

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Basic information

Entry
Database: PDB / ID: 6nel
Title4-(2-(4-fluorophenyl)-5-hydroxy-6-oxo-1,6-dihydropyridin-3-yl)benzoic acid bound to influenza 2009 pH1N1 endonuclease
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN/INHIBITOR / Influenza endonuclease inhibitor chelator / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


viral translational frameshifting / viral RNA genome replication / RNA binding / metal ion binding
Similarity search - Function
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
Chem-KKV / : / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBauman, J.D. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI119321 United States
CitationJournal: Chemmedchem / Year: 2019
Title: Aryl and Arylalkyl Substituted 3-Hydroxypyridin-2(1H)-ones: Synthesis and Evaluation as Inhibitors of Influenza A Endonuclease.
Authors: Sagong, H.Y. / Bauman, J.D. / Nogales, A. / Martinez-Sobrido, L. / Arnold, E. / LaVoie, E.J.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.title ..._citation.journal_abbrev / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)29,0616
Polymers28,5051
Non-polymers5565
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-28 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.250, 101.270, 66.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polymerase acidic protein


Mass: 28505.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 99 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-KKV / 4-[2-(4-fluorophenyl)-5-hydroxy-6-oxo-1,6-dihydropyridin-3-yl]benzoic acid


Mass: 325.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12FNO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: Crystals were formed by mixing in a 1:1 ratio the purified endonuclease protein (5 mg/ml) with crystallization buffer containing 200 mM MES pH 6.7, 27% PEG8000, 200 mM ammonium sulfate, 1 mM ...Details: Crystals were formed by mixing in a 1:1 ratio the purified endonuclease protein (5 mg/ml) with crystallization buffer containing 200 mM MES pH 6.7, 27% PEG8000, 200 mM ammonium sulfate, 1 mM manganese chloride, 10 mM magnesium acetate, 10 mM taurine, and 50 mM sodium fluoride. Crystals matured to full size in one to two weeks at 20 degrees C.
Temp details: 20 degree room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.68→66.53 Å / Num. obs: 32780 / % possible obs: 96.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 36.3 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.064 / Rrim(I) all: 0.156 / Net I/σ(I): 5.6 / Num. measured all: 187362
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.68-1.785.82.77846470.0441.3253.26795.2
5.33-66.535.50.08711570.9890.0410.09898.3

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Processing

Software
NameVersionClassification
Aimless3.3.22data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M5R

4m5r


Resolution: 2→50.635 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.2
RfactorNum. reflection% reflection
Rfree0.2259 985 4.96 %
Rwork0.2046 --
obs0.2057 19858 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 182.39 Å2 / Biso mean: 59.7996 Å2 / Biso min: 26.07 Å2
Refinement stepCycle: final / Resolution: 2→50.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 43 94 1798
Biso mean--52.92 49.1 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111743
X-RAY DIFFRACTIONf_angle_d0.542322
X-RAY DIFFRACTIONf_chiral_restr0.042242
X-RAY DIFFRACTIONf_plane_restr0.006299
X-RAY DIFFRACTIONf_dihedral_angle_d10.4181033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.10550.30251400.28522638277896
2.1055-2.23740.25291450.2342641278696
2.2374-2.41010.23951220.2332678280096
2.4101-2.65260.20611450.21092623276896
2.6526-3.03640.2381380.20642697283597
3.0364-3.82540.22561580.20012741289998
3.8254-50.65120.21081370.18732855299297
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)
14.53091.69310.60824.7519-1.62954.1592-0.53280.6878-0.2674-0.66160.3287-0.12830.40360.15770.19650.545-0.15690.02740.5705-0.00580.357221.569418.4967-18.4065
23.61522.0122-0.21323.2635-0.09290.5552-0.29940.48380.0003-0.41920.042-0.2222-0.21680.52040.18350.3313-0.1139-0.0490.28280.03370.27117.766918.7107-8.7306
31.7234-0.94820.54911.9585-0.10210.48210.2643-0.8702-0.82820.5188-0.294-0.6631.0126-0.27530.43740.7228-0.2058-0.16070.48240.25350.630214.28194.87724.5173
43.1617-0.11.49782.46581.44424.67730.276-0.46020.20630.3854-0.45620.41020.2585-0.64210.00240.3159-0.1140.00340.3279-0.02840.32853.371914.2272-3.6474
52.378-1.417-0.74846.1533-1.92455.84070.1316-0.2251.0425-0.2277-0.3631.0797-0.6534-0.77870.24150.48580.0355-0.08910.3804-0.17280.69644.939526.8306-1.0747
64.74142.3417-1.52942.93020.09234.4466-0.0378-0.32560.585-0.0016-0.09840.2611-0.72950.4536-0.0020.4739-0.1699-0.08840.3984-0.010.403121.077926.0657-1.6532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 31 )A-4 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 49 )A32 - 49
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 83 )A50 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 126 )A84 - 126
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 149 )A127 - 149
6X-RAY DIFFRACTION6chain 'A' and (resid 150 through 195 )A150 - 195

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