+Open data
-Basic information
Entry | Database: PDB / ID: 3iw7 | ||||||
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Title | Human p38 MAP Kinase in Complex with an Imidazo-pyridine | ||||||
Components | Mitogen-activated protein kinase 14 | ||||||
Keywords | TRANSFERASE / DFG-out / Type-I / Alternative splicing / ATP-binding / Cytoplasm / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information stress-activated protein kinase signaling cascade / 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 / cartilage condensation ...stress-activated protein kinase signaling cascade / 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 / cartilage condensation / positive regulation of myoblast fusion / cellular response to UV-B / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / positive regulation of muscle cell differentiation / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / D-glucose import / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / p38MAPK cascade / Regulation of MITF-M-dependent genes involved in pigmentation / fatty acid oxidation / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to dietary excess / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / positive regulation of myoblast differentiation / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / negative regulation of hippo signaling / signal transduction in response to DNA damage / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / p38MAPK events / striated muscle cell differentiation / positive regulation of interleukin-12 production / response to muscle stretch / positive regulation of brown fat cell differentiation / bone development / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / stem cell differentiation / activated TAK1 mediates p38 MAPK activation / positive regulation of D-glucose import / cellular response to ionizing radiation / response to insulin / NOD1/2 Signaling Pathway / placenta development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cellular response to virus / platelet activation / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / chemotaxis / positive regulation of reactive oxygen species metabolic process / cellular senescence / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis / secretory granule lumen / Oxidative Stress Induced Senescence / 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 / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / apoptotic process / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Gruetter, C. / Simard, J.R. / Rauh, D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: High-Throughput Screening To Identify Inhibitors Which Stabilize Inactive Kinase Conformations in p38alpha Authors: Simard, J.R. / Gruetter, C. / Pawar, V. / Aust, B. / Wolf, A. / Rabiller, M. / Wulfert, S. / Robubi, A. / Kluter, S. / Ottmann, C. / Rauh, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iw7.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iw7.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 3iw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iw7_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3iw7_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3iw7_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 3iw7_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/3iw7 ftp://data.pdbj.org/pub/pdb/validation_reports/iw/3iw7 | HTTPS FTP |
-Related structure data
Related structure data | 3iw5C 3iw6C 3iw8C 1zyjS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 41234.973 Da / Num. of mol.: 1 / Mutation: C119S, C162S, A172C, F327L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 / Plasmid: pGEX 6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q16539, mitogen-activated protein kinase | ||||
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#2: Sugar | #3: Chemical | ChemComp-IPK / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM MES, 20-30% PEG 4000, 50mM n-BOG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5417 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 29, 2009 / Details: Osmic |
Radiation | Monochromator: Multilayer Optik / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45 Å / Num. all: 14512 / Num. obs: 14316 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.95 % / Biso Wilson estimate: 36.689 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.61 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 6 / Num. measured obs: 6374 / Num. unique all: 1627 / Num. unique obs: 1592 / % possible all: 97.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO / Packing: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1zyj Resolution: 2.4→37.04 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.173 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.785 / SU B: 9.586 / SU ML: 0.226 / SU R Cruickshank DPI: 0.608 / SU Rfree: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.608 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.04 Å2 / Biso mean: 30.118 Å2 / Biso min: 10.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→37.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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