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- PDB-4bc6: Crystal structure of human serine threonine kinase-10 bound to no... -

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Basic information

Entry
Database: PDB / ID: 4bc6
TitleCrystal structure of human serine threonine kinase-10 bound to novel Bosutinib Isoform 1, previously thought to be Bosutinib
ComponentsSERINE/THREONINE-PROTEIN KINASE 10
KeywordsTRANSFERASE
Function / homology
Function and homology information


lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity ...lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase 10, catalytic domain / Polo kinase kinase / : / Polo kinase kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Serine/threonine-protein kinase 10, catalytic domain / Polo kinase kinase / : / Polo kinase kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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, ATP binding site / Protein kinases ATP-binding region signature. / 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
Chem-XZN / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVollmar, M. / Szklarz, M. / Chaikuad, A. / Elkins, J. / Savitsky, P. / Azeez, K.A. / Salah, E. / Krojer, T. / Canning, P. / Muniz, J.R.C. ...Vollmar, M. / Szklarz, M. / Chaikuad, A. / Elkins, J. / Savitsky, P. / Azeez, K.A. / Salah, E. / Krojer, T. / Canning, P. / Muniz, J.R.C. / Bountra, C. / Arrowsmith, C.H. / von Delft, F. / Weigelt, J. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of Human Serine Threonine Kinase- 10 Bound to Novel Bosutinib Isoform 1, Previously Thought to be Bosutinib
Authors: Vollmar, M. / Szklarz, M. / Chaikuad, A. / Elkins, J. / Savitsky, P. / Azeez, K.A. / Salah, E. / Krojer, T. / Canning, P. / Muniz, J.R.C. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / ...Authors: Vollmar, M. / Szklarz, M. / Chaikuad, A. / Elkins, J. / Savitsky, P. / Azeez, K.A. / Salah, E. / Krojer, T. / Canning, P. / Muniz, J.R.C. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S.
History
DepositionOct 1, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionOct 10, 2012ID: 3ZZ2
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7213
Polymers33,1281
Non-polymers5932
Water79344
1
A: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules

A: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4426
Polymers66,2572
Non-polymers1,1854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area3320 Å2
ΔGint-25.5 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.170, 114.030, 134.340
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 SERINE/THREONINE-PROTEIN KINASE 10 / SERINE THREONINE KINASE-10 / LYMPHOCYTE-ORIENTED KINASE


Mass: 33128.289 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 24-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-LAMBDA-PPASE
References: UniProt: O94804, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-XZN / 4-[(3,5-DICHLORO-4-METHOXYPHENYL)AMINO]-6-METHOXY-7-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]QUINOLINE-3-CARBONITRILE / BOSUTINIB ISOFORM 1


Mass: 530.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29Cl2N5O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.86 Å3/Da / Density % sol: 57.04 % / Description: NONE
Crystal growDetails: 0.1M SPG PH 7.0; 60% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.2→19.18 Å / Num. obs: 20251 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 49.61 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J7T

2j7t


Resolution: 2.2→19.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9047 / SU R Cruickshank DPI: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.201 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.183
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 1038 5.13 %RANDOM
Rwork0.2114 ---
obs0.2136 20250 99.3 %-
Displacement parametersBiso mean: 93.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.6204 Å20 Å20 Å2
2---8.3246 Å20 Å2
3---6.7042 Å2
Refine analyzeLuzzati coordinate error obs: 0.506 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 40 44 2175
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012196HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.083002HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d993SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it2196HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion302SEMIHARMONIC5
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_contact2521SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.32 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2719 150 5.09 %
Rwork0.2578 2797 -
all0.2585 2947 -
obs--99.3 %
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)
14.1835-1.32780.50341.14690.64715.42560.011-0.13370.8337-0.2646-0.0491-0.2091-0.9663-0.14580.038-0.60790.0028-0.00120.52540.001-0.5562-13.084-19.775621.1872
24.38143.4094004.37686.174-0.04030.16320.04850.21420.12710.09270.1669-0.2106-0.0867-0.46330.0485-0.19660.60790.1665-0.5948-30.3856-30.56380.3678
35.30410.07561.20131.57420.66246.57510.13350.1835-0.7851-0.3556-0.18810.25771.0688-0.25290.0545-0.42080.0247-0.07570.6079-0.0204-0.4852-11.5814-40.421617.6808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 25-176
2X-RAY DIFFRACTION2CHAIN A AND RESID 177-208
3X-RAY DIFFRACTION3CHAIN A AND RESID 209-316

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