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- PDB-4mk2: 3-(5-hydroxy-6-oxo-1,6-dihydropyridin-3-yl)benzonitrile bound to ... -

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Basic information

Entry
Database: PDB / ID: 4mk2
Title3-(5-hydroxy-6-oxo-1,6-dihydropyridin-3-yl)benzonitrile bound to influenza 2009 pH1N1 endonuclease
ComponentsPOLYMERASE PA
KeywordsRNA BINDING PROTEIN/INHIBITOR / CAP-SNATCHING / RNA BINDING PROTEIN / RNA BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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
Chem-28B / : / Polymerase acidic protein
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 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)29,0407
Polymers28,5051
Non-polymers5356
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.694, 101.432, 66.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

21A-588-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein POLYMERASE PA


Mass: 28505.270 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: M9V5A4

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Non-polymers , 5 types, 220 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-28B / 3-(5-hydroxy-6-oxo-1,6-dihydropyridin-3-yl)benzonitrile


Mass: 212.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: 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, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 4, 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: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 48860 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.61
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)model building
PHENIX(phenix.refine: dev_1448)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.241 Å / SU ML: 0.19 / σ(F): 28.32 / Phase error: 19.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 1251 5.01 %
Rwork0.1671 --
obs0.1685 48556 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→40.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 28 214 1888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121727
X-RAY DIFFRACTIONf_angle_d1.1362336
X-RAY DIFFRACTIONf_dihedral_angle_d15.662649
X-RAY DIFFRACTIONf_chiral_restr0.045242
X-RAY DIFFRACTIONf_plane_restr0.005295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88780.29551450.28222742X-RAY DIFFRACTION100
1.8878-1.92880.27991450.26112695X-RAY DIFFRACTION100
1.9288-1.97370.24731460.22932733X-RAY DIFFRACTION100
1.9737-2.0230.22121410.2222682X-RAY DIFFRACTION100
2.023-2.07770.27121450.21192731X-RAY DIFFRACTION100
2.0777-2.13890.22581470.19022739X-RAY DIFFRACTION100
2.1389-2.20790.19941420.16672686X-RAY DIFFRACTION100
2.2079-2.28680.21211450.16222712X-RAY DIFFRACTION100
2.2868-2.37840.20621460.1612708X-RAY DIFFRACTION100
2.3784-2.48660.19331450.16122741X-RAY DIFFRACTION100
2.4866-2.61770.19861400.15622703X-RAY DIFFRACTION100
2.6177-2.78160.20141450.16322731X-RAY DIFFRACTION100
2.7816-2.99630.19471400.1572702X-RAY DIFFRACTION100
2.9963-3.29780.21841390.1662724X-RAY DIFFRACTION100
3.2978-3.77460.18781420.15352721X-RAY DIFFRACTION100
3.7746-4.75440.16321390.1352721X-RAY DIFFRACTION100
4.7544-40.2510.16851430.17582650X-RAY DIFFRACTION97
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)
16.53972.72730.1725.2154-1.97094.2106-0.26610.484-0.2146-0.33760.15410.07190.10230.16860.07950.2637-0.07170.0150.275-0.01860.153921.514918.737-18.3006
24.70311.4376-0.12244.3267-0.73343.89770.0253-0.5088-0.5620.1483-0.0871-0.16720.5933-0.05580.08830.2475-0.0848-0.02910.20760.05170.248416.357512.6292-0.5899
31.7331-0.2296-0.71164.8302-2.70373.40420.2211-0.2646-0.78330.1872-0.4242-0.60610.62740.37160.10740.3751-0.084-0.09430.26480.11180.484714.31524.64490.887
43.43280.35491.06582.16551.41685.84890.2167-0.21990.13920.1448-0.37130.4810.3984-0.730.08550.209-0.0599-0.02960.2294-0.01250.25493.419713.933-3.5488
52.17930.1895-4.47546.1891-1.8019.51510.1720.27951.3573-0.0720.0060.9112-1.3164-0.6088-0.17230.46860.0931-0.03870.3133-0.00690.57095.233529.7429-3.1995
62.44780.9341-1.08558.1317-2.07578.4501-0.14690.07540.5495-0.37840.07841.2987-0.4284-1.36230.09230.2410.0064-0.06590.3293-0.06170.36414.851522.93420.8702
73.62241.9648-1.70791.2492-0.55993.9013-0.0076-0.07630.4182-0.0717-0.0620.1443-0.5730.29910.04920.316-0.1147-0.04970.2511-0.01670.248320.772426.0104-1.4656
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 138 )
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 149 )
7X-RAY DIFFRACTION7chain 'A' and (resid 150 through 195 )

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