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- PDB-9tmr: Crystal structure of M. tuberculosis PknA in complex with Stauros... -

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Basic information

Entry
Database: PDB / ID: 9tmr
TitleCrystal structure of M. tuberculosis PknA in complex with Staurosporine
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
STAUROSPORINE / Serine/threonine-protein kinase PknA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)31,0993
Polymers30,5361
Non-polymers5632
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.862, 58.286, 71.320
Angle α, β, γ (deg.)90.000, 98.917, 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-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.95 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.2 M ammonium sulphate, 0.2 M NaCl and 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: 1.9→48.2 Å / Num. obs: 18082 / % possible obs: 97.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.6
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1068 / CC1/2: 0.343

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40.81 Å / SU ML: 0.3099 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.8231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2771 860 4.77 %
Rwork0.2483 17188 -
obs0.2497 18048 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 40 21 1944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01791974
X-RAY DIFFRACTIONf_angle_d1.4832695
X-RAY DIFFRACTIONf_chiral_restr0.0854301
X-RAY DIFFRACTIONf_plane_restr0.016347
X-RAY DIFFRACTIONf_dihedral_angle_d13.8761733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.50051510.50262732X-RAY DIFFRACTION94.49
2.02-2.170.38431420.40712870X-RAY DIFFRACTION97.54
2.17-2.390.3571500.31822866X-RAY DIFFRACTION97.67
2.39-2.740.3111210.27612867X-RAY DIFFRACTION96.39
2.74-3.450.27141600.23162892X-RAY DIFFRACTION98.52
3.45-40.810.21081360.18932961X-RAY DIFFRACTION98.1

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