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- PDB-4ln7: 5,6-bis(4-fluorophenyl)-3-hydroxy-2,5-dihydropyridin-2-one bound ... -

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Basic information

Entry
Database: PDB / ID: 4ln7
Title5,6-bis(4-fluorophenyl)-3-hydroxy-2,5-dihydropyridin-2-one bound to influenza 2009 pH1N1 endonuclease
ComponentsPOLYMERASE PA
KeywordsRNA BINDING PROTEIN/INHIBITOR / CAP-SNATCHING / RNA BINDING PROTEIN-INHIBITOR / RNA BINDING PROTEIN-INHIBITOR complex
Function / homology5,6-bis(4-fluorophenyl)pyridine-2,3-diol / : / :
Function and homology information
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBauman, J.D. / Patel, D. / Das, K. / Arnold, E.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors.
Authors: Bauman, J.D. / Patel, D. / Baker, S.F. / Vijayan, R.S. / Xiang, A. / Parhi, A.K. / Martinez-Sobrido, L. / Lavoie, E.J. / Das, K. / Arnold, E.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Other
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3119
Polymers24,5611
Non-polymers7508
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: POLYMERASE PA
hetero molecules

A: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,62118
Polymers49,1222
Non-polymers1,49916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3480 Å2
ΔGint-102 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.658, 101.049, 66.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein POLYMERASE PA


Mass: 24560.865 Da / Num. of mol.: 1 / Fragment: unp residues 1-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS (A/LIMA/WRAIR1695P/2009(H1N1))
Gene: PA / Plasmid: PCDF-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: F0TRT1

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Non-polymers , 6 types, 165 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-1ZQ / 5,6-bis(4-fluorophenyl)pyridine-2,3-diol


Mass: 299.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11F2NO2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.7
Details: 200 MM MES, 27% PEG8K, 200 MM AMMONIUM SULFATE, 1 MM MANGANESE CHLORIDE, 10 MM MAGNESIUM ACETATE, 10 MM TAURINE, AND 50 MM SODIUM FLUORIDE, pH 6.7, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2012
RadiationMonochromator: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 33413 / Num. obs: 33347 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.056 / Rsym value: 0.063 / Net I/σ(I): 22.76
Reflection shellResolution: 1.73→1.78 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.43 / Rsym value: 0.681 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→33.533 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 1618 5.08 %5%
Rwork0.18 ---
obs0.1812 31857 99.78 %-
all-31927 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→33.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 43 157 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141748
X-RAY DIFFRACTIONf_angle_d1.2932360
X-RAY DIFFRACTIONf_dihedral_angle_d15.407656
X-RAY DIFFRACTIONf_chiral_restr0.075242
X-RAY DIFFRACTIONf_plane_restr0.007298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7301-1.7810.2341310.22692493X-RAY DIFFRACTION100
1.781-1.83850.22391390.21432475X-RAY DIFFRACTION100
1.8385-1.90420.23721270.21072507X-RAY DIFFRACTION100
1.9042-1.98050.25221250.18932502X-RAY DIFFRACTION100
1.9805-2.07060.22311350.17842488X-RAY DIFFRACTION100
2.0706-2.17970.21221480.17132493X-RAY DIFFRACTION100
2.1797-2.31630.18771300.16332517X-RAY DIFFRACTION100
2.3163-2.4950.20111260.17052532X-RAY DIFFRACTION100
2.495-2.7460.20991410.17542505X-RAY DIFFRACTION100
2.746-3.14310.23091200.18092554X-RAY DIFFRACTION100
3.1431-3.9590.20381450.17452548X-RAY DIFFRACTION99
3.959-33.53880.18221510.18432625X-RAY DIFFRACTION99
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)
17.31153.21350.94625.334-1.36455.3393-0.30030.5482-0.2612-0.34740.2418-0.01240.1952-0.03250.00680.2674-0.04220.0310.204-0.03750.142721.654518.7095-18.4479
24.04110.6339-0.63256.2571-2.71896.3595-0.143-0.4394-0.65020.3172-0.1209-0.15750.56-0.09250.34420.2717-0.0877-0.01010.16880.0330.264216.553412.6554-0.7005
32.26961.611-0.43594.4254-3.11775.54710.2614-0.0622-0.9422-0.0251-0.4809-0.80190.68360.69870.13660.3636-0.0647-0.05760.27570.0590.508114.57414.83220.6943
43.41650.75890.62363.03070.66825.08970.2243-0.15240.08310.318-0.20670.50850.3784-0.7526-0.06490.239-0.0507-0.01040.2527-0.01650.25213.56514.2716-3.574
54.92480.4892-1.53176.4884-1.32567.08770.1724-0.05380.6703-0.1043-0.04460.6684-0.7122-0.5581-0.0890.28980.0297-0.03020.1925-0.07810.27338.267325.92441.8351
63.52551.6776-1.87241.8398-0.82344.69570.01870.06080.23980.0066-0.1105-0.0038-0.76660.46230.11310.3409-0.1105-0.03580.2216-0.02430.242624.957826.5851-4.9463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 126 )
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 164 )
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 195 )

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