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- PDB-5i3o: Crystal Structure of BMP-2-inducible kinase in complex with an In... -

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Basic information

Entry
Database: PDB / ID: 5i3o
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 / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding ...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 / 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. ...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-IDV / BMP-2-inducible protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Sao Paulo Research Foundation (FAPESP)2013/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of BMP-2-inducible kinase in complex with an Indazole inhibitor
Authors: Counago, R.M. / Sorrell, F.J. / Krojer, T. / Elkins, J.M. / Gileadi, O. / Willson, T.M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Arruda, P.
History
DepositionFeb 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,0196
Polymers68,0282
Non-polymers9914
Water5,098283
1
A: BMP-2-inducible protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6064
Polymers34,0141
Non-polymers5923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BMP-2-inducible protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4142
Polymers34,0141
Non-polymers3991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.249, 78.249, 255.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsMonomer according to Gel filtration

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Components

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


Mass: 34014.180 Da / Num. of mol.: 2 / 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 (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NSY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-IDV / N-(6-{3-[(dimethylsulfamoyl)amino]phenyl}-1H-indazol-3-yl)cyclopropanecarboxamide


Mass: 399.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N5O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES pH 6; 0.2M ammonium chloride, 20% PEG 8000, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.4→29.56 Å / Num. obs: 31839 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 57.08 Å2 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5 % / Rmerge(I) obs: 0.0478 / Mean I/σ(I) obs: 0.3 / % possible all: 96.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSMarch 1, 2015data reduction
Aimless0.5.17data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W9W

4w9w


Resolution: 2.4→24.71 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.348 / SU Rfree Blow DPI: 0.252 / SU Rfree Cruickshank DPI: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1602 5.05 %RANDOM
Rwork0.193 ---
obs0.196 31738 99 %-
Displacement parametersBiso mean: 67.32 Å2
Baniso -1Baniso -2Baniso -3
1--2.7731 Å20 Å20 Å2
2---2.7731 Å20 Å2
3---5.5462 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.4→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 66 284 5107
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014929HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.136690HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2286SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes125HARMONIC2
X-RAY DIFFRACTIONt_gen_planes738HARMONIC5
X-RAY DIFFRACTIONt_it4929HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion3.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion642SEMIHARMONIC5
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_contact5614SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.48 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.268 141 5.42 %
Rwork0.25 2459 -
obs--90.51 %
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)
14.42731.49531.90714.34750.93684.3380.0027-0.15330.06740.13280.14480.4043-0.1019-0.3129-0.1475-0.03320.11530.06220.1136-0.0179-0.189322.4574-5.098230.3781
23.25731.529-0.40732.3893-0.11032.63550.0925-0.2285-0.36150.3759-0.061-0.24630.1691-0.1816-0.0315-0.03490.01980.00110.0972-0.0213-0.132130.695-15.389529.3454
30.0201-0.64111.75372.77780.44450.2944-0.05770.07370.3259-0.00090.12470.0351-0.0284-0.2229-0.067-0.07210.09430.09160.13780.0211-0.105424.4856-2.8578.3148
41.63580.36440.24423.2429-1.48092.6745-0.0881-0.1838-0.08690.10560.0107-0.0795-0.00770.1360.0774-0.04940.0440.02880.0532-0.0294-0.108737.9431-10.452412.0089
52.5353-0.9743-0.31254.4637-0.41881.2155-0.0461-0.1737-0.5417-0.2375-0.0725-0.46440.432-0.08450.11860.03010.04070.1008-0.0697-0.00450.033835.1816-30.240812.9563
62.99980.5306-0.17952.13270.50921.0962-0.21210.503-0.4621-0.49630.10170.05360.2698-0.01860.1104-0.0149-0.01070.09770.025-0.0854-0.109534.8835-18.3124-1.7811
73.42190.29491.73882.3074-1.18092.952-0.17090.3106-0.2463-0.0133-0.0571-0.46470.03210.07020.228-0.11420.01650.08260.0476-0.0572-0.023447.627-12.4512-0.2123
83.36181.6789-0.05894.9552.27730.13770.0030.26950.4098-0.1710.297-0.1278-0.02210.294-0.30.0401-0.07240.09610.0461-0.0697-0.165311.9054-27.4098-0.2744
94.42681.0052-1.04662.8873-0.62254.6047-0.08740.2022-0.2507-0.31030.2579-0.50370.32580.542-0.1705-0.0360.04580.04530.0402-0.1466-0.141414.0726-40.11780.8869
101.84-0.87480.80350-2.64140-0.004-0.02680.1907-0.2598-0.0166-0.2723-0.0357-0.00590.0206-0.0435-0.06010.05780.0497-0.0839-0.080611.4208-27.321822.7172
112.3859-0.4798-1.81882.4961.2563.0354-0.06830.2237-0.1864-0.23090.0238-0.04310.5417-0.07980.04450.07850.0337-0.0084-0.0138-0.0611-0.17958.4912-43.953917.6883
120.1814-1.7973-1.8840.39671.73641.35670.0129-0.0237-0.1025-0.01650.0139-0.03270.0580.0409-0.02680.16180.1520.10360.0461-0.1496-0.128126.4176-56.979613.6737
132.36390.9215-0.47170-0.41560.1103-0.0375-0.0853-0.3083-0.18090.022-0.27790.32460.30430.01540.10050.152-0.00690.0485-0.0181-0.155718.717-49.879924.7866
144.2163-0.023-0.17323.38420.4122.8033-0.1349-0.3029-0.54190.34520.1185-0.26820.54420.44070.01640.05890.09610.0473-0.0419-0.0131-0.249510.1316-48.00433.0721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|42 - 74}
2X-RAY DIFFRACTION2{A|75 - 131}
3X-RAY DIFFRACTION3{A|132 - 151}
4X-RAY DIFFRACTION4{A|152 - 196}
5X-RAY DIFFRACTION5{A|197 - 244}
6X-RAY DIFFRACTION6{A|245 - 307}
7X-RAY DIFFRACTION7{A|308 - 343}
8X-RAY DIFFRACTION8{B|42 - 74}
9X-RAY DIFFRACTION9{B|75 - 131}
10X-RAY DIFFRACTION10{B|132 - 151}
11X-RAY DIFFRACTION11{B|152 - 208}
12X-RAY DIFFRACTION12{B|209 - 224}
13X-RAY DIFFRACTION13{B|225 - 261}
14X-RAY DIFFRACTION14{B|262 - 343}

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