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- PDB-3fyk: Crystal structure of a benzthiophene lead bound to MAPKAP Kinase-... -

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Basic information

Entry
Database: PDB / ID: 3fyk
TitleCrystal structure of a benzthiophene lead bound to MAPKAP Kinase-2 (MK-2)
ComponentsMAP kinase-activated protein kinase 2
KeywordsTRANSFERASE / MK-2 / MK2 / MAPKAP-2 / Ser/Thr kinase / MAP kinase / Alternative splicing / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase
Function / homology
Function and homology information


macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity ...macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity / mitogen-activated protein kinase binding / regulation of interleukin-6 production / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / Regulation of HSF1-mediated heat shock response / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...MAP kinase activated protein kinase, C-terminal / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-B98 / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKurumbail, R.G. / Caspers, N.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Benzothiophene inhibitors of MK2. Part 2: improvements in kinase selectivity and cell potency.
Authors: Anderson, D.R. / Meyers, M.J. / Kurumbail, R.G. / Caspers, N. / Poda, G.I. / Long, S.A. / Pierce, B.S. / Mahoney, M.W. / Mourey, R.J. / Parikh, M.D.
History
DepositionJan 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
X: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1752
Polymers37,8981
Non-polymers2771
Water00
1
X: MAP kinase-activated protein kinase 2
hetero molecules

X: MAP kinase-activated protein kinase 2
hetero molecules

X: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5256
Polymers113,6933
Non-polymers8323
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation60_665-y+3/2,-z+3/2,x1
crystal symmetry operation78_566z,-x+3/2,-y+3/21
Buried area3720 Å2
ΔGint-23 kcal/mol
Surface area41230 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)254.598, 254.598, 254.598
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein MAP kinase-activated protein kinase 2 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAPK-2 / MK2


Mass: 37897.750 Da / Num. of mol.: 1 / Fragment: MK-2 kinase module and the auto-inhibitory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAP-2, MAPKAPK2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-B98 / (3R)-3-(aminomethyl)-9-methoxy-1,2,3,4-tetrahydro-5H-[1]benzothieno[3,2-e][1,4]diazepin-5-one


Mass: 277.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15N3O2S

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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: 4.54 Å3/Da / Density % sol: 72.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: MK-2 protein at 5 mg/ml equilibrated against a well solution of 1.6 - 2.0 M Sodium malonate at pH 5.4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Mar 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 8772 / % possible obs: 93.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.083 / Χ2: 0.998 / Net I/σ(I): 19.778
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.5-3.626.90.3528600.87795.1
3.62-3.777.20.2718730.88795.3
3.77-3.947.20.2038730.87595
3.94-4.157.40.1668560.87194.4
4.15-4.417.70.1098720.92194.2
4.41-4.757.70.0868810.96493.6
4.75-5.227.80.0788550.97993.1
5.22-5.977.70.0858791.00292.2
5.97-7.57.70.0648931.11491.3
7.5-307.40.0389301.44188.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A06,1ATP,1CDK,2PHK

1a06

1atp

1cdk

2phk


Resolution: 3.5→30 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.277 / WRfactor Rwork: 0.24 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.792 / SU B: 27.133 / SU ML: 0.428 / SU Rfree: 0.568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.568 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 424 4.8 %RANDOM
Rwork0.265 ---
obs0.267 8772 93.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.41 Å2 / Biso mean: 98.046 Å2 / Biso min: 54.67 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 19 0 2317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222365
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9733187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32224.128109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.83415451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4261516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211767
X-RAY DIFFRACTIONr_mcbond_it0.6521.51406
X-RAY DIFFRACTIONr_mcangle_it1.20322283
X-RAY DIFFRACTIONr_scbond_it0.9573959
X-RAY DIFFRACTIONr_scangle_it1.7584.5904
LS refinement shellResolution: 3.498→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 30 -
Rwork0.337 617 -
all-647 -
obs--95.01 %

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