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- PDB-2oic: Crystal structure of IRAK4 kinase domain complexed with staurosporine -

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Basic information

Entry
Database: PDB / ID: 2oic
TitleCrystal structure of IRAK4 kinase domain complexed with staurosporine
ComponentsInterleukin-1 receptor-associated kinase 4
KeywordsTRANSFERASE / kinase
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 / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / interleukin-1 receptor binding / neutrophil mediated immunity ...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 / 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 / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extrinsic component of plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / JNK cascade / positive regulation of smooth muscle cell proliferation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / lipopolysaccharide-mediated signaling pathway / Interleukin-1 signaling / cytokine-mediated signaling pathway / kinase activity / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 / magnesium ion binding / cell surface / extracellular space / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
STAUROSPORINE / Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.4 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)137,6918
Polymers135,8254
Non-polymers1,8664
Water4,846269
1
A: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4232
Polymers33,9561
Non-polymers4671
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)34,4232
Polymers33,9561
Non-polymers4671
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)34,4232
Polymers33,9561
Non-polymers4671
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)34,4232
Polymers33,9561
Non-polymers4671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.894, 141.321, 88.263
Angle α, β, γ (deg.)90.00, 122.27, 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-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.82 %
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: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 62496 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 58.1 Å2 / Rsym value: 7.1 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 6058 / Rsym value: 0.511 / % possible all: 96.7

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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: 2.4→48.17 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 20.094 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 3147 5.1 %RANDOM
Rwork0.22285 ---
obs0.22567 59030 99.86 %-
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: 64.797 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å20 Å21.11 Å2
2---0.87 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8893 0 140 269 9302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229207
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.99712470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51651111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93725.397428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89915.0361657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4391539
X-RAY DIFFRACTIONr_chiral_restr0.1410.21389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026796
X-RAY DIFFRACTIONr_nbd_refined0.20.24047
X-RAY DIFFRACTIONr_nbtor_refined0.2980.26271
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2380
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.28
X-RAY DIFFRACTIONr_mcbond_it0.7321.55733
X-RAY DIFFRACTIONr_mcangle_it1.30228985
X-RAY DIFFRACTIONr_scbond_it1.34734556
X-RAY DIFFRACTIONr_scangle_it2.3044.53485
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 248 -
Rwork0.293 4277 -
obs--99.32 %
Refinement TLS params.Method: refined / Origin x: -26.6581 Å / Origin y: 0.0057 Å / Origin z: -18.7803 Å
111213212223313233
T-0.0507 Å20.0146 Å2-0.0067 Å2--0.1086 Å2-0.0327 Å2---0.0738 Å2
L0.933 °20.1707 °2-0.0068 °2-0.1338 °2-0.0857 °2--0.5017 °2
S-0.0083 Å °0.022 Å °-0.0791 Å °-0.0187 Å °-0.0403 Å °-0.0077 Å °-0.0384 Å °-0.0211 Å °0.0486 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA163 - 4584 - 299
2X-RAY DIFFRACTION1BB164 - 4595 - 300
3X-RAY DIFFRACTION1CC161 - 4582 - 299
4X-RAY DIFFRACTION1DD161 - 4592 - 300

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