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- PDB-6b2p: Dual Inhibition of the Essential Protein Kinases A and B in Mycob... -

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Basic information

Entry
Database: PDB / ID: 6b2p
TitleDual Inhibition of the Essential Protein Kinases A and B in Mycobacterium tuberculosis
ComponentsSerine/threonine-protein kinase PknB
KeywordsTRANSFERASE/INHIBITOR / kinase / drug design / tuberculosis / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of growth rate / protein serine/threonine kinase activity => GO:0004674 / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall ...negative regulation of growth rate / protein serine/threonine kinase activity => GO:0004674 / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion binding / regulation of cell shape / protein autophosphorylation / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / 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. ...PASTA domain / PASTA domain / PASTA domain profile. / PASTA / 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-CJJ / Serine/threonine-protein kinase PknB / Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.01 Å
AuthorsZuccola, H.J.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Mtb PKNA/PKNB Dual Inhibition Provides Selectivity Advantages for Inhibitor Design To Minimize Host Kinase Interactions.
Authors: Wang, T. / Bemis, G. / Hanzelka, B. / Zuccola, H. / Wynn, M. / Moody, C.S. / Green, J. / Locher, C. / Liu, A. / Gao, H. / Xu, Y. / Wang, S. / Wang, J. / Bennani, Y.L. / Thomson, J.A. / Muh, U.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Serine/threonine-protein kinase PknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6842
Polymers30,2871
Non-polymers3971
Water0
1
A: Serine/threonine-protein kinase PknB
hetero molecules

A: Serine/threonine-protein kinase PknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3684
Polymers60,5742
Non-polymers7942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)117.952, 123.146, 45.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Serine/threonine-protein kinase PknB


Mass: 30287.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pknB / Production host: Escherichia coli (E. coli)
References: UniProt: P9WI80, UniProt: P9WI81*PLUS, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CJJ / 5-{5-chloro-4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}thiophene-2-sulfonamide


Mass: 396.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13ClN6O2S2

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) PEGMME 2000, 0.1 M Tris-HCI pH 8.5, 400 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.011→58.976 Å / Num. obs: 6695 / % possible obs: 97.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 110.36 Å2 / Net I/σ(I): 15.1

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PROCESS1.1.7data reduction
PROCESS1.1.7data scaling
BUSTER2.11.7phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.01→58.98 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.837 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.417
RfactorNum. reflection% reflectionSelection details
Rfree0.255 336 5.02 %RANDOM
Rwork0.201 ---
obs0.204 6695 97.7 %-
Displacement parametersBiso mean: 112.79 Å2
Baniso -1Baniso -2Baniso -3
1--21.5729 Å20 Å20 Å2
2--43.3623 Å20 Å2
3----21.7894 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 3.01→58.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 25 0 1992
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092036HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.032774HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d689SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes301HARMONIC5
X-RAY DIFFRACTIONt_it2036HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion21.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion261SEMIHARMONIC5
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_contact2231SEMIHARMONIC4
LS refinement shellResolution: 3.01→3.37 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3504 -4.04 %
Rwork0.2468 1806 -
all0.2508 1882 -
obs--99.63 %
Refinement TLS params.Method: refined / Origin x: 92.9238 Å / Origin y: 78.2034 Å / Origin z: 19.2549 Å
111213212223313233
T-0.0489 Å20.054 Å2-0.152 Å2--0.3036 Å2-0.0052 Å2---0.2651 Å2
L5.1095 °21.1148 °2-2.8411 °2-6.0958 °20.5028 °2--3.6061 °2
S0.0302 Å °0.0109 Å °0.3975 Å °-0.4985 Å °-0.2325 Å °0.5328 Å °-0.2486 Å °-0.0103 Å °0.2023 Å °
Refinement TLS groupSelection details: { A|* }

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