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Open data
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Basic information
Entry | Database: PDB / ID: 5v61 | ||||||
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Title | Phospho-ERK2 bound to bivalent inhibitor SBP2 | ||||||
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![]() | TRANSFERASE/INHIBITOR / kinase / MAPK / phosphorylation / cancer / TRANSFERASE-TRANSFERASE INHIBITOR complex / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | ![]() trans-activation response element binding / Interactions of Tat with host cellular proteins / regulation of translation in response to stress / protein serine/threonine phosphatase inhibitor activity / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of viral transcription / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation ...trans-activation response element binding / Interactions of Tat with host cellular proteins / regulation of translation in response to stress / protein serine/threonine phosphatase inhibitor activity / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of viral transcription / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / phospho-PLA2 pathway / Signaling by MAPK mutants / evasion of host immune response / RAF-independent MAPK1/3 activation / Suppression of apoptosis / molecular sequestering activity / host cell nucleolus / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated / response to epidermal growth factor / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / actinin binding / positive regulation of macrophage proliferation / negative regulation of TOR signaling / Regulation of the apoptosome activity / outer ear morphogenesis / regulation of cellular pH / regulation of Golgi inheritance / Signaling by LTK in cancer / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / 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 / negative regulation of peptidyl-threonine phosphorylation / regulation of cytoskeleton organization / Activation of the AP-1 family of transcription factors / face development / ERK/MAPK targets / progesterone receptor signaling pathway / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / pseudopodium / : / positive regulation of telomere capping / Recycling pathway of L1 / MAPK1 (ERK2) activation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Bergmann glial cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / thyroid gland development / negative regulation of cell differentiation / Advanced glycosylation endproduct receptor signaling / steroid hormone receptor signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / MAP kinase activity / regulation of ossification / Tat-mediated elongation of the HIV-1 transcript / RNA-binding transcription regulator activity / RHO GTPases Activate WASPs and WAVEs / mitogen-activated protein kinase / Formation of HIV-1 elongation complex containing HIV-1 Tat / phosphatase binding / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / Schwann cell development / Growth hormone receptor signaling / stress-activated MAPK cascade / lipopolysaccharide-mediated signaling pathway / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / NPAS4 regulates expression of target genes / ERK1 and ERK2 cascade / protein serine/threonine/tyrosine kinase activity / myelination / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / cellular response to amino acid starvation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lechtenberg, B.C. / Riedl, S.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Guided Strategy for the Development of Potent Bivalent ERK Inhibitors. Authors: Lechtenberg, B.C. / Mace, P.D. / Sessions, E.H. / Williamson, R. / Stalder, R. / Wallez, Y. / Roth, G.P. / Riedl, S.J. / Pasquale, E.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.3 KB | Display | ![]() |
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PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5v60C ![]() 5v62C ![]() 2erkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AI
#1: Protein | Mass: 41258.172 Da / Num. of mol.: 1 / Fragment: UNP residues 8-367 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P28482, mitogen-activated protein kinase |
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#2: Protein/peptide | Mass: 3529.271 Da / Num. of mol.: 1 Fragment: UNP Q15418 residues 713-729, UNP P04608 residues 730-738 Source method: obtained synthetically / Details: RSK1 peptide Source: (synth.) ![]() ![]() References: UniProt: Q15418, UniProt: P04608, non-specific serine/threonine protein kinase |
-Non-polymers , 4 types, 97 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/FRZ.gif)
![](data/chem/img/90A.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FRZ.gif)
![](data/chem/img/90A.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-FRZ / | #5: Chemical | ChemComp-90A / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | Ligand 90A links FRZ and inhibitor RSK1 peptide to form bivalent ERK inhibitor SBP2 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 45% v/v polypropylene glycol P400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.82 Å / Num. obs: 26480 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.569 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ERK Resolution: 2.2→19.82 Å / SU B: 12.483 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.17 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 60.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.82 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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