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Open data
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Basic information
Entry | Database: PDB / ID: 5byz | ||||||
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Title | ERK5 in complex with small molecule | ||||||
![]() | Mitogen-activated protein kinase 7 | ||||||
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Function / homology | ![]() Signalling to ERK5 / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / calcineurin-NFAT signaling cascade / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / ERKs are inactivated / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, H. / Tucker, J. / Wang, X. / Gavine, P.R. / Philips, C. / Augustin, M.A. / Schreiner, P. / Steinbacher, S. / Preston, M. / Ogg, D. | ||||||
![]() | ![]() Title: Discovery of a novel allosteric inhibitor-binding site in ERK5: comparison with the canonical kinase hinge ATP-binding site. Authors: Chen, H. / Tucker, J. / Wang, X. / Gavine, P.R. / Phillips, C. / Augustin, M.A. / Schreiner, P. / Steinbacher, S. / Preston, M. / Ogg, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.7 KB | Display | ![]() |
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PDB format | ![]() | 134.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 39826.855 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, unp residues 48-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q13164, ![]() | ||
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#2: Chemical | ChemComp-4WE / | ||
#3: Chemical | ChemComp-GOL / ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.05 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 11 % PEG4000 0.01 M MgCl2 0.18 M Na-Formiate 0.10 M MES, pH=6.50 0.01 M Tris/Cl, pH=8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.65→72.82 Å / Num. obs: 62385 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 24.22 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 7 % / Rmerge(I) obs: 0.069 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.515 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→72.82 Å
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Refine LS restraints |
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