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- PDB-8ozz: PH domain of AKT-like kinase in Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 8ozz
TitlePH domain of AKT-like kinase in Trypanosoma cruzi
ComponentsPH domain of Akt-like kinase in Trypanosoma cruzi
KeywordsLIPID BINDING PROTEIN / PH domain / AKT-like/RAC/PKB / kinase / Trypanosoma cruzi
Function / homology
Function and homology information


phosphorylation / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Serine/Threonine Kinase AGC, catalytic domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Protein kinase domain ...Serine/Threonine Kinase AGC, catalytic domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / 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
Similarity search - Domain/homology
Rac serine-threonine kinase, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodSOLUTION NMR / na
AuthorsStadler, K.A. / Ortiz-Joya, L.J. / Zangger, K. / Gubensaek, N.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundFWF T-1239 Austria
Austrian Science FundDOC 50 Austria
CitationJournal: Sci Rep / Year: 2024
Title: Structural investigation of Trypanosoma cruzi Akt-like kinase as drug target against Chagas disease.
Authors: Stadler, K.A. / Ortiz-Joya, L.J. / Singh Sahrawat, A. / Buhlheller, C. / Gruber, K. / Pavkov-Keller, T. / O'Hagan, T.B. / Guarne, A. / Pulido, S. / Marin-Villa, M. / Zangger, K. / Gubensak, N.
History
DepositionMay 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PH domain of Akt-like kinase in Trypanosoma cruzi


Theoretical massNumber of molelcules
Total (without water)13,4941
Polymers13,4941
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PH domain of Akt-like kinase in Trypanosoma cruzi


Mass: 13494.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053509047.110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4D6D3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HNCO
131isotropic13D HN(CO)CA
141isotropic13D HN(CA)CO
151isotropic13D HN(COCA)CB
171isotropic13D HN(CA)CB
161isotropic13D H(CCO)NH
183isotropic13D (H)CCH-TOCSY
1103isotropic13D 1H-13C NOESY
1113isotropic12D 1H-13C HSQC
191isotropic13D 1H-15N NOESY
1121isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-13C; U-15N] PH domain of AKT-like kinase in Trypanosoma cruzi, 50 mM KPi, 100 mM NaCl, 90% H2O/10% D2O15N-/13C-labeled sample 0.5 mM90% H2O/10% D2O
solution30.46 mM [U-13C; U-15N] PH domain of AKT-like kinase in Trypanosoma cruzi, 50 mM KPi, 100 mM NaCl, 100% D2O15N-/13C-labeled sample in D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPH domain of AKT-like kinase in Trypanosoma cruzi[U-13C; U-15N]1
50 mMKPinone1
100 mMNaClnone1
0.46 mMPH domain of AKT-like kinase in Trypanosoma cruzi[U-13C; U-15N]3
50 mMKPinone3
100 mMNaClnone3
Sample conditionsIonic strength: 100,08 mM / Label: Conditions / pH: 6.5 / Pressure: 1,01325 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz / Details: TCI Cryo Probe 5 mm

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2.CCPNchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNdata analysis
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
RefinementMethod: na / Software ordinal: 2 / Details: fragment selection and full-atom relaxation
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 10

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