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- PDB-2pzy: Structure of MK2 Complexed with Compound 76 -

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Basic information

Entry
Database: PDB / ID: 2pzy
TitleStructure of MK2 Complexed with Compound 76
ComponentsMAP kinase-activated protein kinase 2
KeywordsTRANSFERASE / MK2 / 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 / 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 / calmodulin-dependent protein kinase activity ...macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / 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 / calmodulin-dependent protein kinase activity / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / regulation of interleukin-6 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 / MAPK cascade / positive regulation of tumor necrosis factor production / 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 / Protein kinase, ATP binding site ...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-B18 / STAUROSPORINE / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWhite, A. / Wu, J.P. / Wang, J. / Abeywardane, A. / Andersen, D. / Emmanuel, M. / Gautschi, E. / Goldberg, D.R. / Kashem, M.A. / Lukas, S. ...White, A. / Wu, J.P. / Wang, J. / Abeywardane, A. / Andersen, D. / Emmanuel, M. / Gautschi, E. / Goldberg, D.R. / Kashem, M.A. / Lukas, S. / Mao, W. / Martin, L. / Morwick, T. / Moss, N. / Pargellis, C. / Patel, U.R. / Patnaude, L. / Peet, G.W. / Skow, D. / Snow, R.J. / Ward, Y. / Werneburg, B.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: The discovery of carboline analogs as potent MAPKAP-K2 inhibitors
Authors: Wu, J.-P. / Wang, J. / Abeywardane, A. / Andersen, D. / Emmanuel, M. / Gautschi, E. / Goldberg, D.R. / Kashem, M.A. / Lukas, S. / Mao, W. / Martin, L. / Morwick, T. / Moss, N. / Pargellis, C. ...Authors: Wu, J.-P. / Wang, J. / Abeywardane, A. / Andersen, D. / Emmanuel, M. / Gautschi, E. / Goldberg, D.R. / Kashem, M.A. / Lukas, S. / Mao, W. / Martin, L. / Morwick, T. / Moss, N. / Pargellis, C. / Patel, U.R. / Patnaude, L. / Peet, G.W. / Skow, D. / Snow, R.J. / Ward, Y. / Werneburg, B. / White, A.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,4337
Polymers150,0854
Non-polymers1,3483
Water0
1
A: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9622
Polymers37,5211
Non-polymers4411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9622
Polymers37,5211
Non-polymers4411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9882
Polymers37,5211
Non-polymers4671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,5211
Polymers37,5211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
hetero molecules

A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
hetero molecules

A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,29921
Polymers450,25612
Non-polymers4,0439
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area56530 Å2
ΔGint-285 kcal/mol
Surface area141560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)159.610, 159.610, 134.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Detailsbiological unit is the monomer; there are four distinct biological units in the asym.

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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: 37521.332 Da / Num. of mol.: 4 / Fragment: MAPK-Activated protein kinase 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-B18 / (4R)-N-[4-({[2-(DIMETHYLAMINO)ETHYL]AMINO}CARBONYL)-1,3-THIAZOL-2-YL]-4-METHYL-1-OXO-2,3,4,9-TETRAHYDRO-1H-BETA-CARBOLINE-6-CARBOXAMIDE


Mass: 440.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N6O3S
#3: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM

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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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 1.85 M AMMONIUM SULFATE, vapor diffusion, hanging drop, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 8, 2005 / Details: Osmics confocal blue optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→34.32 Å / Num. all: 42263 / Num. obs: 42263 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.109 / Χ2: 1 / Net I/σ(I): 8.2 / Scaling rejects: 960
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.8 / Num. measured all: 10846 / Num. unique all: 4042 / Χ2: 0.65 / % possible all: 94.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata processing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→34.32 Å / FOM work R set: 0.74 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.313 2118 RANDOM
Rwork0.251 --
all-42263 -
obs-42263 -
Displacement parametersBiso mean: 73.012 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9488 0 97 0 9585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 42

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.9-2.920.41470.369893940
2.92-2.950.378430.36934977
2.95-2.970.334630.352906969
2.97-30.36480.339916964
3-3.030.423410.341949990
3.03-3.050.401360.336946982
3.05-3.080.416470.33917964
3.08-3.110.364510.318922973
3.11-3.140.385420.336946988
3.14-3.180.398500.323942992
3.18-3.210.379540.319935989
3.21-3.240.357550.303913968
3.24-3.280.346350.314949984
3.28-3.320.437470.327950997
3.32-3.360.391390.2959851024
3.36-3.40.359490.287935984
3.4-3.450.291560.263931987
3.45-3.490.433580.2879741032
3.49-3.540.336480.2589881036
3.54-3.60.328540.241939993
3.6-3.650.319500.2349501000
3.65-3.710.336480.2399791027
3.71-3.780.297710.2039311002
3.78-3.850.321440.2439701014
3.85-3.920.304630.2269521015
3.92-40.296460.219901036
4-4.090.331530.2229651018
4.09-4.180.331500.2289811031
4.18-4.290.31400.2329781018
4.29-4.40.302540.2129641018
4.4-4.530.3600.1999861046
4.53-4.680.302450.2099701015
4.68-4.850.255490.1989811030
4.85-5.040.21510.1969751026
5.04-5.270.355570.2629721029
5.27-5.550.351580.279761034
5.55-5.90.376490.2889891038
5.9-6.350.353510.2689821033
6.35-6.990.271530.2399801033
6.99-80.27540.2319941048
8-10.080.265590.2189701029
10.08-500.010.213500.244940990

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