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Open data
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Basic information
Entry | Database: PDB / ID: 6f3d | ||||||
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Title | IRAK4 IN COMPLEX WITH inhibitor | ||||||
![]() | Interleukin-1 receptor-associated kinase 4![]() | ||||||
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Function / homology | ![]() IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / neutrophil migration / interleukin-33-mediated signaling pathway / toll-like receptor 9 signaling pathway / neutrophil mediated immunity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xue, Y. / Degorce, S.L. / Robb, G.R. / Ferguson, A.D. | ||||||
![]() | ![]() Title: Optimization of permeability in a series of pyrrolotriazine inhibitors of IRAK4. Authors: Degorce, S.L. / Anjum, R. / Dillman, K.S. / Drew, L. / Groombridge, S.D. / Halsall, C.T. / Lenz, E.M. / Lindsay, N.A. / Mayo, M.F. / Pink, J.H. / Robb, G.R. / Scott, J.S. / Stokes, S. / Xue, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.8 KB | Display | ![]() |
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PDB format | ![]() | 198.3 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: 33315.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The residues names TPO & SEP are the phosphorylated form of THR and SER, respectively. The protein has been phosphorylated during protein expression/production. Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9NWZ3, ![]() #2: Chemical | ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.31 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion Details: 50 mM Hepes pH 7.5, 0.02% octylglucoside, 10% glycerol, 0.3 M NaCl, 1 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.38→94.12 Å / Num. obs: 31282 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 57.88 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.38→2.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7 |
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Processing
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Refinement | Resolution: 2.38→94.12 Å / Cor.coef. Fo:Fc: 0.9362 / Cor.coef. Fo:Fc free: 0.9181 / SU R Cruickshank DPI: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.206 / SU Rfree Cruickshank DPI: 0.208
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Displacement parameters | Biso mean: 63.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.336 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→94.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.46 Å / Total num. of bins used: 16
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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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