|Entry||Database: PDB / ID: 3d83|
|Title||Crystal structure of P38 kinase in complex with a biphenyl amide inhibitor|
|Components||Mitogen-activated protein kinase 14MAPK14|
|Keywords||TRANSFERASE / P38 / SERINE/THREONINE PROTEIN KINASE / MAP KINASE / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase|
|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 / 3'-UTR-mediated mRNA stabilization / stress-induced premature senescence / transmembrane receptor protein serine/threonine kinase signaling pathway / negative regulation of hippo signaling / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions ...positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / 3'-UTR-mediated mRNA stabilization / stress-induced premature senescence / transmembrane receptor protein serine/threonine kinase signaling pathway / negative regulation of hippo signaling / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / Platelet sensitization by LDL / cartilage condensation / cellular response to UV-B / stress-activated protein kinase signaling cascade / positive regulation of myoblast fusion / mitogen-activated protein kinase p38 binding / positive regulation of muscle cell differentiation / positive regulation of myotube differentiation / Myogenesis / glucose import / NFAT protein binding / p38MAPK cascade / response to dietary excess / ERK/MAPK targets / Activation of the AP-1 family of transcription factors / regulation of cytokine production involved in inflammatory response / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / chondrocyte differentiation / regulation of ossification / positive regulation of myoblast differentiation / MAP kinase activity / mitogen-activated protein kinase / MAP kinase kinase activity / stress-activated MAPK cascade / vascular endothelial growth factor receptor signaling pathway / skeletal muscle tissue development / cellular response to vascular endothelial growth factor stimulus / positive regulation of cardiac muscle cell proliferation / signal transduction in response to DNA damage / negative regulation of inflammatory response to antigenic stimulus / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / lipopolysaccharide-mediated signaling pathway / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / DNA damage checkpoint signaling / positive regulation of erythrocyte differentiation / stem cell differentiation / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / positive regulation of glucose import / placenta development / negative regulation of canonical Wnt signaling pathway / bone development / ADP signalling through P2Y purinoceptor 1 / NOD1/2 Signaling Pathway / response to insulin / platelet activation / cellular response to virus / osteoblast differentiation / spindle pole / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / cell morphogenesis / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / chemotaxis / cellular senescence / cellular response to tumor necrosis factor / Oxidative Stress Induced Senescence / secretory granule lumen / angiogenesis / cellular response to lipopolysaccharide / protein phosphatase binding / Regulation of TP53 Activity through Phosphorylation / peptidyl-serine 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 / regulation of transcription by RNA polymerase II / positive regulation of gene expression / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding
Similarity search - Function
Mitogen-activated protein kinase 14 / 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 ...Mitogen-activated protein kinase 14 / 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
Chem-GK6 / Mitogen-activated protein kinase 14
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å|
|Citation||Journal: Bioorg.Med.Chem.Lett. / Year: 2008|
Title: Biphenyl amide p38 kinase inhibitors 4: DFG-in and DFG-out binding modes.
Authors: Angell, R.M. / Angell, T.D. / Bamborough, P. / Bamford, M.J. / Chung, C.W. / Cockerill, S.G. / Flack, S.S. / Jones, K.L. / Laine, D.I. / Longstaff, T. / Ludbrook, S. / Pearson, R. / Smith, K. ...Authors: Angell, R.M. / Angell, T.D. / Bamborough, P. / Bamford, M.J. / Chung, C.W. / Cockerill, S.G. / Flack, S.S. / Jones, K.L. / Laine, D.I. / Longstaff, T. / Ludbrook, S. / Pearson, R. / Smith, K.J. / Smee, P.A. / Somers, D.O. / Walker, A.L.
|Structure viewer||Molecule: |
Downloads & links
A: Mitogen-activated protein kinase 14
|#1: Protein|| |
Mass: 41375.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BRL
References: UniProt: Q16539, mitogen-activated protein kinase
|#2: Chemical|| ChemComp-GK6 / |
|#3: Chemical|| ChemComp-GOL / |
|#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 3.07 Å3/Da / Density % sol: 59.97 %|
Description: THE BINARY COMPLEX HAS BEEN FORMED BY SOAKING AN APO-CRYSTAL
|Crystal grow||Temperature: 293 K / Method: vapor diffusion / pH: 6.5 |
Details: Authors suggest to see publication for details, pH 6.5, VAPOR DIFFUSION, temperature 293K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å|
|Detector||Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2001|
|Radiation||Monochromator: Daresbury / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.87 Å / Relative weight: 1|
|Reflection||Resolution: 1.9→35 Å / Num. obs: 34124 / % possible obs: 82.4 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.053 / Χ2: 0.992 / Net I/σ(I): 12.9|
|Reflection shell||Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2939 / Χ2: 0.905 / % possible all: 72.2|
|Refinement||Method to determine structure: FOURIER SYNTHESIS|
Starting model: PDB entry 1WFC
Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.596 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
|Solvent computation||Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK|
|Displacement parameters||Biso mean: 35.516 Å2|
|Refinement step||Cycle: LAST / Resolution: 1.9→20 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 1.9→1.949 Å / Total num. of bins used: 20 |
|Refinement TLS params.|
Method: refined / Refine-ID: X-RAY DIFFRACTION
|Refinement TLS group|
-Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
- Version 3 of the EMDB header file is now the official format.
- The previous official version 1.9 will be removed from the archive.
Related info.:EMDB header
External links:wwPDB to switch to version 3 of the EMDB data model
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
+Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi