+Open data
-Basic information
Entry | Database: PDB / ID: 6ges | ||||||
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Title | Crystal structure of ERK1 covalently bound to SM1-71 | ||||||
Components | Mitogen-activated protein kinase 3 | ||||||
Keywords | TRANSFERASE / kinase / covalent inhibitor / MAPK / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information positive regulation of xenophagy / xenophagy / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / caveolin-mediated endocytosis / cardiac neural crest cell development involved in heart development / response to epidermal growth factor / ERKs are inactivated ...positive regulation of xenophagy / xenophagy / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / caveolin-mediated endocytosis / cardiac neural crest cell development involved in heart development / response to epidermal growth factor / ERKs are inactivated / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / positive regulation of cyclase activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / Regulation of the apoptosome activity / regulation of cellular pH / outer ear morphogenesis / cartilage development / regulation of Golgi inheritance / Signaling by LTK in cancer / interleukin-1-mediated signaling pathway / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / lung morphogenesis / response to exogenous dsRNA / MAPK3 (ERK1) activation / pseudopodium / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / regulation of cytoskeleton organization / face development / : / RUNX2 regulates osteoblast differentiation / positive regulation of telomere capping / Bergmann glial cell differentiation / thyroid gland development / Advanced glycosylation endproduct receptor signaling / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / Regulation of HSF1-mediated heat shock response / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / signal transduction in response to DNA damage / mitogen-activated protein kinase / RHO GTPases Activate WASPs and WAVEs / phosphatase binding / BMP signaling pathway / Signal attenuation / Schwann cell development / Nuclear events stimulated by ALK signaling in cancer / peptidyl-tyrosine autophosphorylation / phosphorylation / Growth hormone receptor signaling / lipopolysaccharide-mediated signaling pathway / stress-activated MAPK cascade / negative regulation of TORC1 signaling / positive regulation of telomere maintenance via telomerase / phosphotyrosine residue binding / sensory perception of pain / cellular response to cadmium ion / NPAS4 regulates expression of target genes / myelination / cellular response to amino acid starvation / ERK1 and ERK2 cascade / RNA Polymerase I Promoter Opening / NCAM signaling for neurite out-growth / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / Regulation of PTEN gene transcription / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Signaling by high-kinase activity BRAF mutants / Spry regulation of FGF signaling / MAP2K and MAPK activation / modulation of chemical synaptic transmission / caveola / Oncogene Induced Senescence / Regulation of actin dynamics for phagocytic cup formation / ISG15 antiviral mechanism / cellular response to mechanical stimulus / cellular response to reactive oxygen species / Negative regulation of MAPK pathway / Signaling by RAF1 mutants Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Chaikuad, A. / Suman, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gray, N.S. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Cell Chem Biol / Year: 2019 Title: Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome. Authors: Rao, S. / Gurbani, D. / Du, G. / Everley, R.A. / Browne, C.M. / Chaikuad, A. / Tan, L. / Schroder, M. / Gondi, S. / Ficarro, S.B. / Sim, T. / Kim, N.D. / Berberich, M.J. / Knapp, S. / Marto, ...Authors: Rao, S. / Gurbani, D. / Du, G. / Everley, R.A. / Browne, C.M. / Chaikuad, A. / Tan, L. / Schroder, M. / Gondi, S. / Ficarro, S.B. / Sim, T. / Kim, N.D. / Berberich, M.J. / Knapp, S. / Marto, J.A. / Westover, K.D. / Sorger, P.K. / Gray, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ges.cif.gz | 300.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ges.ent.gz | 242.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ges.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ges_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6ges_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6ges_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 6ges_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/6ges ftp://data.pdbj.org/pub/pdb/validation_reports/ge/6ges | HTTPS FTP |
-Related structure data
Related structure data | 6ateC 6g54C 4qtbS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 25 - 374 / Label seq-ID: 26 - 375
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43277.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK3, ERK1, PRKM3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 References: UniProt: P27361, mitogen-activated protein kinase |
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-Non-polymers , 5 types, 322 molecules
#2: Chemical | #3: Chemical | ChemComp-EWH / ~{ | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow | Temperature: 277.14 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 34% PEG 4k, 0.2M Li2SO4, 0.1M tris 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99986 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99986 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→47.02 Å / Num. obs: 44884 / % possible obs: 98.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 35.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.07→2.13 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2 / Num. unique obs: 3496 / CC1/2: 0.799 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4qtb Resolution: 2.07→47.02 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.836 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.171 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.749 Å2
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Refinement step | Cycle: 1 / Resolution: 2.07→47.02 Å
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Refine LS restraints |
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