[English] 日本語
Yorodumi- PDB-2z7l: Unphosphorylated Mitogen Activated Protein Kinase ERK2 in Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z7l | ||||||
---|---|---|---|---|---|---|---|
Title | Unphosphorylated Mitogen Activated Protein Kinase ERK2 in Complex with (4-{[5-Carbamoyl-4-(3-Methylanilino)Pyrimidin 2-Yl]Amino}Phenyl)Acetic Acid | ||||||
Components | Mitogen-activated protein kinase 1 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CELL CYCLE / PHOSPHORYLATION / Acetylation / Nucleotide-binding | ||||||
Function / homology | Function and homology information phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs ...phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs / Transcriptional and post-translational regulation of MITF-M expression and activity / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of actin dynamics for phagocytic cup formation / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Signaling by Activin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / diadenosine tetraphosphate biosynthetic process / Recycling pathway of L1 / neural crest cell development / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / mitogen-activated protein kinase kinase kinase binding / positive regulation of macrophage proliferation / outer ear morphogenesis / regulation of cellular pH / Thrombin signalling through proteinase activated receptors (PARs) / regulation of Golgi inheritance / RAF/MAP kinase cascade / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Neutrophil degranulation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / : / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / lung morphogenesis / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / progesterone receptor signaling pathway / androgen receptor signaling pathway / pseudopodium / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of telomere capping / Bergmann glial cell differentiation / thyroid gland development / negative regulation of cell differentiation / decidualization / steroid hormone receptor signaling pathway / cellular response to cadmium ion / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / phosphatase binding / Schwann cell development / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / sensory perception of pain / positive regulation of telomere maintenance via telomerase / ERK1 and ERK2 cascade / myelination / dendrite cytoplasm / phosphotyrosine residue binding / cellular response to amino acid starvation / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / caveola / positive regulation of translation / long-term synaptic potentiation Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Katayama, N. / Kurihara, H. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Identification of a key element for hydrogen-bonding patterns between protein kinases and their inhibitors Authors: Katayama, N. / Orita, M. / Yamaguchi, T. / Hisamichi, H. / Kuromitsu, S. / Kurihara, H. / Sakashita, H. / Matsumoto, Y. / Fujita, S. / Niimi, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2z7l.cif.gz | 86 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2z7l.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 2z7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z7l_validation.pdf.gz | 771.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2z7l_full_validation.pdf.gz | 785.4 KB | Display | |
Data in XML | 2z7l_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2z7l_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/2z7l ftp://data.pdbj.org/pub/pdb/validation_reports/z7/2z7l | HTTPS FTP |
-Related structure data
Related structure data | 2z8cC 3erkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42361.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mapk1, Erk2, Mapk, Prkm1 / Plasmid: pET28b / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P63086, mitogen-activated protein kinase | ||
---|---|---|---|
#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-S91 / [ | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.59 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: PEG550 MME, ethylene glycol, beta-mercaptoethanol, pH7.0, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 6, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44.31 Å / Num. obs: 12389 / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.077 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ERK Resolution: 2.41→44.31 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 397568.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.13 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→44.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
|