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Yorodumi- PDB-2lgc: Joint NMR and X-ray refinement reveals the structure of a novel d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lgc | ||||||
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Title | Joint NMR and X-ray refinement reveals the structure of a novel dibenzo[a,d]cycloheptenone inhibitor/p38 MAP kinase complex in solution | ||||||
Components | Mitogen-activated protein kinase 14 | ||||||
Keywords | TRANSFERASE / P38 MAPK kinase-inhibitor complex / hybrid NMR/X-ray structure | ||||||
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 / DSCAM interactions / 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 / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / glucose import / 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 / 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 / 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 interleukin-12 production / positive regulation of brown fat cell differentiation / 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 / positive regulation of glucose import / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / placenta development / 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 / 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 / Oxidative Stress Induced Senescence / secretory granule lumen / 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 | SOLUTION NMR / torsion angle dynamics, sampling | ||||||
Model details | best R-free, model 1 | ||||||
Authors | Habeck, M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2012 Title: Inferential NMR/X-ray-based structure determination of a dibenzo[a,d]cycloheptenone inhibitor-p38alpha MAP kinase complex in solution Authors: Honndorf, V.S. / Coudevylle, N. / Laufer, S. / Becker, S. / Griesinger, C. / Habeck, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lgc.cif.gz | 645.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lgc.ent.gz | 540 KB | Display | PDB format |
PDBx/mmJSON format | 2lgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lgc_validation.pdf.gz | 415.5 KB | Display | wwPDB validaton report |
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Full document | 2lgc_full_validation.pdf.gz | 486.6 KB | Display | |
Data in XML | 2lgc_validation.xml.gz | 75.7 KB | Display | |
Data in CIF | 2lgc_validation.cif.gz | 99.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/2lgc ftp://data.pdbj.org/pub/pdb/validation_reports/lg/2lgc | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 41208.141 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 / Production host: Escherichia coli (E. coli) References: UniProt: Q16539, mitogen-activated protein kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM [U-13C; U-15N; U-2H] P38, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1 mM / Component: P38-1 / Isotopic labeling: [U-13C; U-15N; U-2H] |
Sample conditions | Ionic strength: 150 / pH: 7.4 / Pressure: ambient / Temperature: 25 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 900 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, sampling / Software ordinal: 1 Details: JOINT NMR AND X-RAY REFINEMENT WITH NMR RESTRAINTS AND X-RAY REFLECTIONS FROM PDB ENTRY 3ZYA. | |||||||||||||||
NMR representative | Selection criteria: best r-free | |||||||||||||||
NMR ensemble | Conformer selection criteria: lowest R-free / Conformers calculated total number: 3000 / Conformers submitted total number: 10 |