+Open data
-Basic information
Entry | Database: PDB / ID: 3new | ||||||
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Title | p38-alpha complexed with Compound 10 | ||||||
Components | Mitogen-activated protein kinase 14MAPK14 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / Ser/Thr kinase / Intracellular / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cartilage condensation ...positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cartilage condensation / cellular response to UV-B / Platelet sensitization by LDL / stress-activated protein kinase signaling cascade / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / positive regulation of muscle cell differentiation / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / glucose import / response to dietary excess / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / regulation of ossification / MAP kinase activity / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / signal transduction in response to DNA damage / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / positive regulation of cardiac muscle cell proliferation / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / placenta development / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / negative regulation of canonical Wnt signaling pathway / response to insulin / NOD1/2 Signaling Pathway / bone development / cell morphogenesis / platelet activation / osteoblast differentiation / cellular response to virus / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / chemotaxis / cellular senescence / cellular response to tumor necrosis factor / protein phosphatase binding / peptidyl-serine phosphorylation / angiogenesis / Oxidative Stress Induced Senescence / secretory granule lumen / cellular response to lipopolysaccharide / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / transcription by RNA polymerase II / cell surface receptor signaling pathway / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Goedken, E.R. / Comess, K.M. / Sun, C. / Argiriadi, M. / Jia, Y. / Quinn, C.M. / Banach, D.L. / Marcotte, D. / Borhani, D. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2011 Title: Discovery and Characterization of Non-ATP Site Inhibitors of the Mitogen Activated Protein (MAP) Kinases. Authors: Comess, K.M. / Sun, C. / Abad-Zapatero, C. / Goedken, E.R. / Gum, R.J. / Borhani, D.W. / Argiriadi, M. / Groebe, D.R. / Jia, Y. / Clampit, J.E. / Haasch, D.L. / Smith, H.T. / Wang, S. / ...Authors: Comess, K.M. / Sun, C. / Abad-Zapatero, C. / Goedken, E.R. / Gum, R.J. / Borhani, D.W. / Argiriadi, M. / Groebe, D.R. / Jia, Y. / Clampit, J.E. / Haasch, D.L. / Smith, H.T. / Wang, S. / Song, D. / Coen, M.L. / Cloutier, T.E. / Tang, H. / Cheng, X. / Quinn, C. / Liu, B. / Xin, Z. / Liu, G. / Fry, E.H. / Stoll, V. / Ng, T.I. / Banach, D. / Marcotte, D. / Burns, D.J. / Calderwood, D.J. / Hajduk, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3new.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3new.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 3new.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/3new ftp://data.pdbj.org/pub/pdb/validation_reports/ne/3new | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41982.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2 / Production host: Escherichia coli (E. coli) References: UniProt: Q16539, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-3NE / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.14 % |
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Crystal grow | Temperature: 291 K / pH: 8 Details: 30 mg/mL protein in 25 mM Tris pH 8, 100 mM NaCl, 10% glycerol, and 10 mM DTT co-crystallized with 1 mM Compound 10 in 20% PEG 2000MME and 0.1 M Bis-Tris pH 6.5 at 18 C., VAPOR DIFFUSION, ...Details: 30 mg/mL protein in 25 mM Tris pH 8, 100 mM NaCl, 10% glycerol, and 10 mM DTT co-crystallized with 1 mM Compound 10 in 20% PEG 2000MME and 0.1 M Bis-Tris pH 6.5 at 18 C., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.51→49.88 Å / Num. obs: 12654 / % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→49.88 Å / Occupancy max: 1 / Occupancy min: 0
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Displacement parameters | Biso mean: 43.98 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→49.88 Å
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