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- PDB-5ikw: Crystal Structure of BMP-2-inducible kinase in complex with an In... -

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Basic information

Entry
Database: PDB / ID: 5ikw
TitleCrystal Structure of BMP-2-inducible kinase in complex with an Indazole inhibitor
ComponentsBMP-2-inducible protein kinase
KeywordsTransferase/Transferase Inhibitor / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
Function / homology
Function and homology information


phosphatase regulator activity / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / regulation of bone mineralization / positive regulation of Notch signaling pathway / non-specific serine/threonine protein kinase / phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity ...phosphatase regulator activity / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / regulation of bone mineralization / positive regulation of Notch signaling pathway / non-specific serine/threonine protein kinase / phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
BMP-2-inducible protein kinase, C-terminal / BMP-2-inducible protein kinase C-terminus / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain ...BMP-2-inducible protein kinase, C-terminal / BMP-2-inducible protein kinase C-terminus / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6BU / BMP-2-inducible protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsCounago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. ...Counago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. / Willson, T.M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Arruda, P. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
FAPESP2013/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of BMP-2-inducible kinase in complex with a 3-acylaminoindazole inhibitor GSK3236425A
Authors: Counago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. / Willson, T.M. / Arrowsmith, C.H. / Edwards, A.M. / ...Authors: Counago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. / Willson, T.M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Arruda, P. / Gileadi, O. / Structural Genomics Consortium (SGC)
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BMP-2-inducible protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1872
Polymers34,7911
Non-polymers3961
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.957, 111.155, 164.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein BMP-2-inducible protein kinase / BIKe


Mass: 34791.035 Da / Num. of mol.: 1 / Fragment: UNP residues 38-345 / Mutation: K320A, K321A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2K, BIKE, HRIHFB2017 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NSY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-6BU / N-(6-{3-[(cyclopropylsulfonyl)amino]phenyl}-1H-indazol-3-yl)cyclopropanecarboxamide


Mass: 396.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% (v/v) Broad MW PEG smear; 3.2 M MgCl2, 100 mM Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→29.56 Å / Num. obs: 87521 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 52.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.8 % / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W9W

4w9w


Resolution: 2.41→21.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.299 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.208
RfactorNum. reflection% reflectionSelection details
Rfree0.216 747 4.93 %RANDOM
Rwork0.176 ---
obs0.178 15146 99 %-
Displacement parametersBiso mean: 53.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.8587 Å20 Å20 Å2
2---3.5352 Å20 Å2
3---10.3938 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.41→21.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 28 89 2434
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012399HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043258HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1110SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes363HARMONIC5
X-RAY DIFFRACTIONt_it2399HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion3.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion314SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2686SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.58 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 140 5.27 %
Rwork0.197 2515 -
obs--97.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.689-1.5349-0.6674.82680.03124.35480.07650.2284-0.5323-0.4726-0.26080.32310.3039-0.31060.18430.0085-0.0525-0.1097-0.2112-0.02460.012-0.29869.700336.4172
24.2398-1.62092.03050.13151.44490.38690.02210.03870.0543-0.2055-0.0604-0.03570.12590.08950.03820.19660.14470.02480.06250.1077-0.120711.753816.205926.1593
32.4718-0.63991.0783.2275-0.97152.85470.15180.1937-0.2688-0.1828-0.09080.11510.4274-0.058-0.061-0.0076-0.00770.0115-0.13890.0165-0.1098-0.392118.851133.082
42.7248-0.0883-1.28842.73380.62554.63070.0920.12940.06470.1208-0.0769-0.11010.24020.3986-0.01520.01620.11790.007-0.00880.0551-0.09652.751832.733626.9654
54.43530.4688-0.98070.8007-2.66940.60020.12620.2149-0.1317-0.1316-0.22270.02040.35320.26960.09650.04430.11660.0226-0.03110.0283-0.13223.848426.517227.4684
60.9128-2.7512-0.11182.7325-0.61370.8065-0.00830.0349-0.0470.08890.0353-0.05590.09090.0447-0.02690.28720.1520.10360.0713-0.0048-0.24266.986720.67577.5182
73.634-0.3277-1.68751.92130.21096.2838-0.11310.36680.0053-0.10890.10240.11360.2592-0.5420.0107-0.05920.0870.01690.04560.054-0.1885-5.487333.783414.5115
82.389-0.90140.08772.4322-0.223.79620.0130.12910.5203-0.058-0.168-0.148-0.53550.37690.155-0.03240.05290.0302-0.05480.0783-0.0222.645745.720521.7752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|42 - 85}
2X-RAY DIFFRACTION2{A|86 - 102}
3X-RAY DIFFRACTION3{A|103 - 151}
4X-RAY DIFFRACTION4{A|152 - 185}
5X-RAY DIFFRACTION5{A|186 - 208}
6X-RAY DIFFRACTION6{A|209 - 224}
7X-RAY DIFFRACTION7{A|225 - 287}
8X-RAY DIFFRACTION8{A|288 - 338}

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