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- PDB-3gp0: Crystal Structure of Human Mitogen Activated Protein Kinase 11 (p... -

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Basic information

Entry
Database: PDB / ID: 3gp0
TitleCrystal Structure of Human Mitogen Activated Protein Kinase 11 (p38 beta) in complex with Nilotinib
ComponentsMitogen-activated protein kinase 11
KeywordsTransferase/Transferase Inhibitor / mitogen-activated protein kinase 11 / P38B / P38BETA / PRKM11 / SAPK2 / SAPK2B / stress-activated protein kinase-2 / structural genomics consortium / SGC / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / Transferase-Transferase Inhibitor COMPLEX
Function / homology
Function and homology information


negative regulation of cardiac muscle cell proliferation / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cardiac muscle cell proliferation / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cellular response to UV-B / positive regulation of muscle cell differentiation / Myogenesis / Activation of the AP-1 family of transcription factors ...negative regulation of cardiac muscle cell proliferation / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cardiac muscle cell proliferation / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cellular response to UV-B / positive regulation of muscle cell differentiation / Myogenesis / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / p38MAPK cascade / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / mitogen-activated protein kinase / cellular response to interleukin-1 / stress-activated MAPK cascade / p38MAPK events / positive regulation of interleukin-12 production / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / bone development / cellular response to virus / VEGFA-VEGFR2 Pathway / osteoblast differentiation / cellular senescence / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
Nilotinib / Mitogen-activated protein kinase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsFilippakopoulos, P. / Barr, A. / Fedorov, O. / Keates, T. / Soundararajan, M. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Ugochukwu, E. / Pike, A.C.W. ...Filippakopoulos, P. / Barr, A. / Fedorov, O. / Keates, T. / Soundararajan, M. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Ugochukwu, E. / Pike, A.C.W. / Muniz, J. / Roos, A. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Mitogen Activated Protein Kinase 11 (p38 beta) in complex with Nilotinib
Authors: Filippakopoulos, P. / Barr, A. / Fedorov, O. / Keates, T. / Soundararajan, M. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Ugochukwu, E. / Pike, A.C.W. / Muniz, J. / Roos, A. / Chaikuad, A. ...Authors: Filippakopoulos, P. / Barr, A. / Fedorov, O. / Keates, T. / Soundararajan, M. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Ugochukwu, E. / Pike, A.C.W. / Muniz, J. / Roos, A. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Mitogen-activated protein kinase 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3794
Polymers39,7521
Non-polymers6273
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.940, 60.080, 148.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase 11 / MAPK11 / Mitogen-activated protein kinase p38 beta / MAP kinase p38 beta / p38b / p38-2 / Stress- ...MAPK11 / Mitogen-activated protein kinase p38 beta / MAP kinase p38 beta / p38b / p38-2 / Stress-activated protein kinase 2


Mass: 39752.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK11, PRKM11, SAPK2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: Q15759, mitogen-activated protein kinase
#2: Chemical ChemComp-NIL / Nilotinib / 4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide


Mass: 529.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H22F3N7O / Comment: medication*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 3350 0.1M citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9253 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9253 Å / Relative weight: 1
ReflectionResolution: 1.9→49.51 Å / Num. all: 28422 / Num. obs: 28422 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4091 / Rsym value: 0.654 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.76 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.21 Å
Translation2.5 Å38.21 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble comprising of 2GTN, 1P38, 1LEZ, 1BMK, 3FC1

2gtn

1p38
PDB Unreleased entry

1lez

1bmk

3fc1


Resolution: 1.9→49.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.172 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.868 / SU B: 6.967 / SU ML: 0.097 / SU R Cruickshank DPI: 0.151 / SU Rfree: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1432 5 %RANDOM
Rwork0.178 ---
all0.181 28350 --
obs0.181 28361 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.51 Å2 / Biso mean: 11.775 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 44 211 2898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222779
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9843776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6975335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78523.78127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12115475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.21520
X-RAY DIFFRACTIONr_chiral_restr0.1080.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212103
X-RAY DIFFRACTIONr_mcbond_it3.26131675
X-RAY DIFFRACTIONr_mcangle_it4.43652706
X-RAY DIFFRACTIONr_scbond_it6.8181104
X-RAY DIFFRACTIONr_scangle_it8.286111067
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 115 -
Rwork0.246 1980 -
all-2095 -
obs--99.95 %
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)
12.042.55831.5095.01512.48482.2048-0.0952-0.12850.23530.03320.02380.358-0.0722-0.21530.07150.08060.03240.00510.11820.03130.0815.0362.64634.045
22.12240.0889-2.17210.4914-0.33114.20480.1632-0.17180.20.1731-0.03630.068-0.20880.1505-0.12690.08-0.0270.01590.0264-0.01070.083524.72861.51421.268
33.7883-0.10850.80891.3827-0.32881.4637-0.03310.2156-0.1834-0.11350.03590.10880.1087-0.0512-0.00280.0298-0.00790.00970.0224-0.00790.030921.47759.9960.447
42.9699-0.3226-0.90984.20510.74533.9834-0.14940.11230.0478-0.1127-0.0170.23770.0946-0.24130.16640.087-0.0203-0.03210.07430.07250.155812.37945.04930.619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 76
2X-RAY DIFFRACTION2A77 - 168
3X-RAY DIFFRACTION3A169 - 320
4X-RAY DIFFRACTION4A321 - 348

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