+Open data
-Basic information
Entry | Database: PDB / ID: 1kv2 | ||||||
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Title | Human p38 MAP Kinase in Complex with BIRB 796 | ||||||
Components | p38 MAP kinaseP38 mitogen-activated protein kinases | ||||||
Keywords | TRANSFERASE / protein-inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / 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 ...positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / 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 / 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 / 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 dietary excess / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / signal transduction in response to DNA damage / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of inflammatory response to antigenic stimulus / 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 / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / placenta development / positive regulation of glucose import / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / platelet activation / cellular response to virus / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / 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 / peptidyl-serine phosphorylation / protein phosphatase binding / secretory granule lumen / Oxidative Stress Induced Senescence / angiogenesis / Regulation of TP53 Activity through Phosphorylation / cellular response to lipopolysaccharide / 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 / isomorphous to 1IAN / Resolution: 2.8 Å | ||||||
Authors | Pargellis, C. / Tong, L. / Churchill, L. / Cirillo, P.F. / Gilmore, T. / Graham, A.G. / Grob, P.M. / Hickey, E.R. / Moss, N. / Pav, S. / Regan, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site. Authors: Pargellis, C. / Tong, L. / Churchill, L. / Cirillo, P.F. / Gilmore, T. / Graham, A.G. / Grob, P.M. / Hickey, E.R. / Moss, N. / Pav, S. / Regan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kv2.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kv2.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kv2 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kv2 | 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: 41343.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: Q16539, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-B96 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 30% PEG1500, 5 mM DTT, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21-25 ℃ / Method: vapor diffusion / Details: Pav, S., (1997) Protein Sci., 6, 242. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 13, 1998 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 9700 / Num. obs: 8717 / % possible obs: 90 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 66 |
Reflection | *PLUS Num. measured all: 22129 / Rmerge(I) obs: 0.053 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous to 1IAN / Resolution: 2.8→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 1 / Rfactor obs: 0.228 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |