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- PDB-6n8g: IRAK4 bound to benzoxazole compound -

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Basic information

Entry
Database: PDB / ID: 6n8g
TitleIRAK4 bound to benzoxazole compound
ComponentsInterleukin-1 receptor-associated kinase 4IRAK4
Keywordstransferase/transferase inhibitor / Protein Kinase / IRAK4 / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


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 / interleukin-1 receptor binding ...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 / interleukin-1 receptor binding / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / extrinsic component of plasma membrane / JNK cascade / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of smooth muscle cell proliferation / Interleukin-1 signaling / cytokine-mediated signaling pathway / PIP3 activates AKT signaling / kinase activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / endosome membrane / non-specific serine/threonine protein kinase / intracellular signal transduction / phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / cell surface / extracellular space / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-KFD / Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLarsen, N.A. / Bloudoff, K. / Subramanian, V. / Dobrzanska, M. / Gluza, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
European Regional Development FundUDA-POIG.01.04.00-12-049/11-00 Poland
CitationJournal: To Be Published
Title: To be published
Authors: Larsen, N.A. / Gluza, K.
History
DepositionNov 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-1 receptor-associated kinase 4
B: Interleukin-1 receptor-associated kinase 4
C: Interleukin-1 receptor-associated kinase 4
D: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,3108
Polymers134,2154
Non-polymers2,0944
Water8,935496
1
A: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0772
Polymers33,5541
Non-polymers5241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0772
Polymers33,5541
Non-polymers5241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0772
Polymers33,5541
Non-polymers5241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0772
Polymers33,5541
Non-polymers5241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.955, 141.927, 88.095
Angle α, β, γ (deg.)90.000, 124.580, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Interleukin-1 receptor-associated kinase 4 / IRAK4 / IRAK-4 / Renal carcinoma antigen NY-REN-64


Mass: 33553.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-KFD / N-[2-(morpholin-4-yl)-6-(piperidin-1-yl)-1,3-benzoxazol-5-yl]-6-(1H-pyrrolo[2,3-b]pyridin-5-yl)pyridine-2-carboxamide


Mass: 523.586 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H29N7O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 1.6-1.7 M Sodium Malonate, pH 7.0, 100-150 mM Sodium acetate, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 97136 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.036 / Rrim(I) all: 0.071 / Χ2: 1.053 / Net I/σ(I): 9.6 / Num. measured all: 370550
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 % / % possible all: 100

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2-2.070.76296530.6610.4550.8891.097
2.07-2.150.51696850.8030.3070.6011.077
2.15-2.250.35997130.8960.2140.4191.074
2.25-2.370.25296480.9450.1490.2941.059
2.37-2.520.1797280.9740.1010.1981.06
2.52-2.710.1296810.9860.0710.1391.021
2.71-2.990.07697190.9940.0450.0891.059
2.99-3.420.06197280.9950.0360.0711.023
3.42-4.310.05297420.9950.0310.061.031
4.31-500.03198390.9980.0190.0371.028

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→90.6 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.285 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 4894 5 %RANDOM
Rwork0.1743 ---
obs0.1767 92238 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.19 Å2 / Biso mean: 49.999 Å2 / Biso min: 25.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→90.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8995 0 156 497 9648
Biso mean--40.57 52.26 -
Num. residues----1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0199354
X-RAY DIFFRACTIONr_bond_other_d0.0030.028575
X-RAY DIFFRACTIONr_angle_refined_deg2.0851.99412650
X-RAY DIFFRACTIONr_angle_other_deg1.1893.00519978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36951139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17625.327428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.939151654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.11540
X-RAY DIFFRACTIONr_chiral_restr0.1450.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210259
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021761
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 356 -
Rwork0.279 6658 -
all-7014 -
obs--97.85 %

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