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- PDB-2jbo: Protein kinase MK2 in complex with an inhibitor (crystal form-1, ... -

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Basic information

Entry
Database: PDB / ID: 2jbo
TitleProtein kinase MK2 in complex with an inhibitor (crystal form-1, soaking)
ComponentsMAP KINASE-ACTIVATED PROTEIN KINASE 2
KeywordsTRANSFERASE / SER-THR KINASE / MAPKAP KINASE 2 / PHOSPHORYLATION / MK2 / KINASE / ATP SITE / ATP-BINDING / SERINE/THREONINE-PROTEIN KINASE / SMALL MOLECULE INHIBITOR / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / CREB phosphorylation / macropinocytosis / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / 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 ...calcium-dependent protein serine/threonine kinase activity / CREB phosphorylation / macropinocytosis / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / 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 / regulation of interleukin-6 production / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / cellular response to vascular endothelial growth factor stimulus / Regulation of HSF1-mediated heat shock response / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / response to cytokine / regulation of mRNA stability / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / ciliary basal body / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / centrosome / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...MAP kinase activated protein kinase, C-terminal / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-P4O / PHOSPHATE ION / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsHillig, R.C. / Eberspaecher, U. / Monteclaro, F. / Huber, M. / Nguyen, D. / Mengel, A. / Muller-Tiemann, B. / Egner, U.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural Basis for a High Affinity Inhibitor Bound to Protein Kinase Mk2.
Authors: Hillig, R.C. / Eberspaecher, U. / Monteclaro, F. / Huber, M. / Nguyen, D. / Mengel, A. / Muller-Tiemann, B. / Egner, U.
#1: Journal: Protein Sci. / Year: 2006
Title: Identifying Protein Construct Variants with Increased Crystallization Propensity--A Case Study.
Authors: Malawski, G.A. / Hillig, R.C. / Monteclaro, F. / Eberspaecher, U. / Schmitz, A.A. / Crusius, K. / Huber, M. / Egner, U. / Donner, P. / Muller-Tiemann, B.
History
DepositionDec 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAP KINASE-ACTIVATED PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1013
Polymers37,6651
Non-polymers4352
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)253.959, 253.959, 253.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 37665.461 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 41-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-P4O / 2-(2-QUINOLIN-3-YLPYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE


Mass: 340.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL RESIDUES GLY-SER ARE CLONING ARTIFACTS FROM A THROMBIN CLEAVAGE SITE AFTER GST TAG REMOVAL

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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: 4.5 Å3/Da / Density % sol: 72.9 % / Description: NONE
Crystal growpH: 4.5
Details: 1.5-1.6M SODIUM POTASSIUM PHOSPHATE PH 4.5, 0.014M DEOXY-BIGCHAP. THE INHIBITOR WAS SOAKED INTO CRYSTALS GROWN INITIALLY FROM MK2-ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99991
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99991 Å / Relative weight: 1
ReflectionResolution: 3.1→48.9 Å / Num. obs: 13232 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 87.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.1
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1NY3

1ny3


Resolution: 3.1→48.9 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.866 / SU B: 28.333 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.679 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 722 5.5 %RANDOM
Rwork0.23 ---
obs0.232 12482 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 72.47 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 31 9 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222473
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9833342
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2655293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.47223.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.5515453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.5821516
X-RAY DIFFRACTIONr_chiral_restr0.1140.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021850
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.21107
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.21665
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8631.51507
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50422397
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.01331099
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.514.5945
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 54
Rwork0.223 900
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)
14.78430.4666-1.45041.76261.49345.59190.0223-0.0374-0.38930.13660.0153-0.17420.14790.0894-0.0376-0.1885-0.04620.0351-0.24890.146-0.2734227.96485.253175.232
23.3801-0.2646-0.65714.241-0.29546.4132-0.0881-0.3879-0.10830.34250.1146-0.36780.25170.5975-0.0265-0.1462-0.00490.0447-0.01590.0774-0.1607229.56486.331202.325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 141
2X-RAY DIFFRACTION2A142 - 346

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