+Open data
-Basic information
Entry | Database: PDB / ID: 1ian | ||||||
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Title | HUMAN P38 MAP KINASE INHIBITOR COMPLEX | ||||||
Components | P38 MAP KINASE | ||||||
Keywords | SERINE/THREONINE-PROTEIN KINASE / PROTEIN SER/THR-KINASE / SERINE-THREONINE-PROTEIN KINASE 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 / cartilage condensation ...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 / 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 / glucose import / Activation of the AP-1 family of transcription factors / negative regulation of hippo signaling / 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 / response to dietary excess / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / signal transduction in response to DNA damage / positive regulation of myoblast differentiation / 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 / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / placenta development / activated TAK1 mediates p38 MAPK activation / positive regulation of glucose import / stem cell differentiation / cellular response to ionizing radiation / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cellular senescence / platelet activation / cellular response to virus / spindle pole / VEGFA-VEGFR2 Pathway / 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 response to tumor necrosis factor / peptidyl-serine phosphorylation / protein phosphatase binding / Regulation of TP53 Activity through Phosphorylation / cellular response to lipopolysaccharide / Oxidative Stress Induced Senescence / angiogenesis / secretory granule lumen / 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 / regulation of transcription by RNA polymerase II / Neutrophil degranulation / positive regulation of gene expression / apoptotic process / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SE-MET MAD, molecular replacement / Resolution: 2 Å | ||||||
Authors | Tong, L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: A highly specific inhibitor of human p38 MAP kinase binds in the ATP pocket. Authors: Tong, L. / Pav, S. / White, D.M. / Rogers, S. / Crane, K.M. / Cywin, C.L. / Brown, M.L. / Pargellis, C.A. #1: Journal: FEBS Lett. / Year: 1995 Title: Sb 203580 is a Specific Inhibitor of a Map Kinase Homologue which is Stimulated by Cellular Stresses and Interleukin-1 Authors: Cuenda, A. / Rouse, J. / Doza, Y.N. / Meier, R. / Cohen, P. / Gallagher, T.F. / Young, P.R. / Lee, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ian.cif.gz | 27 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ian.ent.gz | 13.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ian.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ian_validation.pdf.gz | 494.5 KB | Display | wwPDB validaton report |
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Full document | 1ian_full_validation.pdf.gz | 498.6 KB | Display | |
Data in XML | 1ian_validation.xml.gz | 2 KB | Display | |
Data in CIF | 1ian_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/1ian ftp://data.pdbj.org/pub/pdb/validation_reports/ia/1ian | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42105.004 Da / Num. of mol.: 1 / Mutation: N-TERMINAL HIS-TAG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: B834 / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) PLYSS References: UniProt: Q16539, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | |||||||||||||||||||||||||
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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Aug 31, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 25453 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 7 / Rsym value: 0.157 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 179632 |
-Processing
Software |
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Refinement | Method to determine structure: SE-MET MAD, molecular replacement Starting model: ERK2 Resolution: 2→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 28 Å2
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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