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- PDB-9tmx: Crystal structure of M. tuberculosis PknA in complex with AZD-5438 -

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Basic information

Entry
Database: PDB / ID: 9tmx
TitleCrystal structure of M. tuberculosis PknA in complex with AZD-5438
ComponentsSerine/threonine-protein kinase PknA
KeywordsTRANSFERASE / Protein kinase A / PknA / MTb / inhibitor complex
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / negative regulation of lipid biosynthetic process / regulation of fatty acid metabolic process / negative regulation of fatty acid biosynthetic process / regulation of cell shape / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / extracellular region ...peptidyl-threonine autophosphorylation / negative regulation of lipid biosynthetic process / regulation of fatty acid metabolic process / negative regulation of fatty acid biosynthetic process / regulation of cell shape / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Chem-FB8 / Serine/threonine-protein kinase PknA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPollaniemi, A. / Haikarainen, T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Microbiol Spectr / Year: 2026
Title: Structural insights into multitargeting Mycobacterium tuberculosis Pkn kinases.
Authors: Pollaniemi, A. / Miao, Y. / Laitila, L. / Piippo, H. / Hammaren, M. / Parikka, M. / Haikarainen, T.
History
DepositionDec 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PknA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0043
Polymers30,5361
Non-polymers4682
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.960, 58.811, 73.479
Angle α, β, γ (deg.)90.000, 96.090, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

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Components

#1: Protein Serine/threonine-protein kinase PknA


Mass: 30536.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pknA, Rv0015c, MTCY10H4.15c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WI83, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-FB8 / 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine


Mass: 371.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.1-1.2 M ammonium sulphate, 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→47.78 Å / Num. obs: 26965 / % possible obs: 99.5 % / Redundancy: 7 % / Biso Wilson estimate: 26.17 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.5
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 1443 / CC1/2: 0.526

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.16 Å / SU ML: 0.1981 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 1248 4.63 %
Rwork0.2121 25704 -
obs0.2128 26952 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.68 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 31 84 2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621997
X-RAY DIFFRACTIONf_angle_d0.6472725
X-RAY DIFFRACTIONf_chiral_restr0.0423305
X-RAY DIFFRACTIONf_plane_restr0.0046359
X-RAY DIFFRACTIONf_dihedral_angle_d14.152733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.27361190.30692879X-RAY DIFFRACTION99.67
1.77-1.850.33621140.30262876X-RAY DIFFRACTION99.93
1.85-1.950.2791520.28092822X-RAY DIFFRACTION99.7
1.95-2.070.2551510.22962839X-RAY DIFFRACTION99.67
2.07-2.230.24151450.22692836X-RAY DIFFRACTION98.68
2.23-2.450.25091280.21552805X-RAY DIFFRACTION98
2.45-2.810.221320.20862889X-RAY DIFFRACTION99.97
2.81-3.540.23541610.20362862X-RAY DIFFRACTION99.87
3.54-41.160.18821460.18622896X-RAY DIFFRACTION98.8

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