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Open data
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Basic information
Entry | Database: PDB / ID: 5lar | ||||||
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Title | Crystal structure of p38 alpha MAPK14 in complex with VPC00628 | ||||||
![]() | Mitogen-activated protein kinase 14![]() | ||||||
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Function / homology | ![]() DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence ...DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaikuad, A. / Petersen, L.K. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Novel p38alpha MAP kinase inhibitors identified from yoctoReactor DNA-encoded small molecule library Authors: Petersen, L.K. / Blakskaer, P. / Chaikuad, A. / Christensen, A.B. / Dietvorst, J. / Holmkvist, J. / Knapp, S. / Korinek, M. / Larsen, L.K. / Pedersen, A.E. / Rohm, S. / Slok, F.A. / Hansen, N.J.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.9 KB | Display | ![]() |
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PDB format | ![]() | 128.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4looS 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
#1: Protein | ![]() Mass: 41395.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P47811, ![]() |
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#2: Chemical | ChemComp-6SH / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.28 % |
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Crystal grow![]() | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 15% medium-molecular weight PEG Smears (MMW PEG smears), 0.1 M MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→25.7 Å / Num. obs: 58904 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.1 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4LOO Resolution: 1.5→25.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.709 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.076 / 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: 24.966 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→25.7 Å
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Refine LS restraints |
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