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- PDB-2oid: Crystal structure of IRAK4 kinase domain complexed with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 2oid
TitleCrystal structure of IRAK4 kinase domain complexed with AMPPNP
ComponentsInterleukin-1 receptor-associated kinase 4
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


MyD88 dependent cascade initiated on endosome / IRAK4 deficiency (TLR5) / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / interleukin-1 receptor binding / neutrophil mediated immunity ...MyD88 dependent cascade initiated on endosome / IRAK4 deficiency (TLR5) / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / interleukin-1 receptor binding / neutrophil mediated immunity / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / extrinsic component of plasma membrane / toll-like receptor signaling pathway / JNK cascade / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of smooth muscle cell proliferation / cytokine-mediated signaling pathway / Interleukin-1 signaling / PIP3 activates AKT signaling / kinase activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / endosome membrane / intracellular signal transduction / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / cell surface / magnesium ion binding / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.3 Å
AuthorsKuglstatter, A. / Villasenor, A.G. / Browner, M.F.
CitationJournal: J.Immunol. / Year: 2007
Title: Cutting Edge: IL-1 Receptor-Associated Kinase 4 Structures Reveal Novel Features and Multiple Conformations.
Authors: Kuglstatter, A. / Villasenor, A.G. / Shaw, D. / Lee, S.W. / Tsing, S. / Niu, L. / Song, K.W. / Barnett, J.W. / Browner, M.F.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)137,8508
Polymers135,8254
Non-polymers2,0254
Water5,026279
1
A: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4622
Polymers33,9561
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4622
Polymers33,9561
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4622
Polymers33,9561
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4622
Polymers33,9561
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.116, 138.973, 89.198
Angle α, β, γ (deg.)90.00, 126.43, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains 4 kinase-ligand complexes, each of which represents one biological unit.

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Components

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


Mass: 33956.195 Da / Num. of mol.: 4 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Production host: unidentified baculovirus
References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.3M sodium malonate, 0.1M sodium acetate, 0.01M DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97943 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 63527 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Biso Wilson estimate: 50.8 Å2 / Rsym value: 0.112 / Net I/σ(I): 8.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 2OIB

2oib


Resolution: 2.3→49.94 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / SU B: 21.997 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29542 3217 5.1 %RANDOM
Rwork0.24096 ---
obs0.24381 60299 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.347 Å2
Baniso -1Baniso -2Baniso -3
1-2.63 Å20 Å20.75 Å2
2---2.31 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8518 0 124 279 8921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228786
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.99411883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66351057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91125.235405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34415.0381583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3721539
X-RAY DIFFRACTIONr_chiral_restr0.0880.21330
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026416
X-RAY DIFFRACTIONr_nbd_refined0.2180.24417
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2432
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.2112
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.510.25
X-RAY DIFFRACTIONr_mcbond_it0.7111.55483
X-RAY DIFFRACTIONr_mcangle_it1.2428598
X-RAY DIFFRACTIONr_scbond_it1.51133687
X-RAY DIFFRACTIONr_scangle_it2.4534.53285
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 215 -
Rwork0.338 4381 -
obs--97.85 %
Refinement TLS params.Method: refined / Origin x: 22.1556 Å / Origin y: -16.4864 Å / Origin z: 17.7119 Å
111213212223313233
T-0.0631 Å2-0.0182 Å20.0092 Å2--0.0864 Å20.0213 Å2---0.0816 Å2
L0.6089 °2-0.0866 °20.0617 °2-0.3969 °20.1137 °2--0.5947 °2
S-0.0222 Å °-0.1038 Å °-0.0928 Å °0.015 Å °-0.0039 Å °0.0001 Å °-0.1012 Å °0.1283 Å °0.0262 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA164 - 4585 - 299
2X-RAY DIFFRACTION1BB164 - 4595 - 300
3X-RAY DIFFRACTION1CC166 - 4587 - 299
4X-RAY DIFFRACTION1DD164 - 4595 - 300

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