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- PDB-12ob: Crystal Structure of serine/threonine-protein kinase (AEK1) from ... -

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Basic information

Entry
Database: PDB / ID: 12ob
TitleCrystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with AMP
ComponentsPutative rac serine-threonine kinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / serine/threonine-protein kinase
Function / homology
Function and homology information


protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Serine/Threonine Kinase AGC, catalytic domain / 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Serine/threonine protein kinase, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with AMP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative rac serine-threonine kinase
B: Putative rac serine-threonine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1534
Polymers83,4592
Non-polymers6942
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-36 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.187, 85.187, 192.702
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative rac serine-threonine kinase


Mass: 41729.266 Da / Num. of mol.: 2 / Fragment: residues 123-474 / Mutation: T185I, V227F, N314S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_45g89 / Plasmid: TrcrB.01480.a.WW4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4E2L0
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
Has ligand of interestY
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 3.0M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. Cocrystallization with 4mM ATP and 4mM MgCl2. Crystals were soaked overnight in 10 mM AMP solubilized in 3.0M Malonate, ...Details: 3.0M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. Cocrystallization with 4mM ATP and 4mM MgCl2. Crystals were soaked overnight in 10 mM AMP solubilized in 3.0M Malonate, pH 5.0 (cryo solution) which displaced the ATP. plate Liu-S-198, Puck: PSL-0201, Cryo: 3.0M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 30, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.83→48.44 Å / Num. obs: 20044 / % possible obs: 99.9 % / Redundancy: 19.9 % / CC1/2: 1 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.027 / Rrim(I) all: 0.119 / Χ2: 1.2 / Net I/σ(I): 20.9 / Num. measured all: 398469
Reflection shellResolution: 2.83→2.9 Å / % possible obs: 100 % / Redundancy: 21.3 % / Rmerge(I) obs: 2.009 / Num. measured all: 30325 / Num. unique obs: 1427 / CC1/2: 0.906 / Rpim(I) all: 0.445 / Rrim(I) all: 2.058 / Χ2: 1.03 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5936: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→48.44 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 973 4.89 %
Rwork0.2314 --
obs0.234 19916 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.83→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 46 0 5194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045328
X-RAY DIFFRACTIONf_angle_d0.717238
X-RAY DIFFRACTIONf_dihedral_angle_d12.1741921
X-RAY DIFFRACTIONf_chiral_restr0.045783
X-RAY DIFFRACTIONf_plane_restr0.006920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.980.35641300.31342624X-RAY DIFFRACTION99
2.98-3.170.39751390.29772669X-RAY DIFFRACTION99
3.17-3.410.37561590.30692647X-RAY DIFFRACTION99
3.41-3.750.33591140.25752685X-RAY DIFFRACTION99
3.75-4.30.29761280.22912714X-RAY DIFFRACTION100
4.3-5.410.25731480.22738X-RAY DIFFRACTION100
5.41-48.440.23121550.21062866X-RAY DIFFRACTION100
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)
10.23410.2437-0.12250.349-0.26320.22270.05430.204-0.1523-0.4297-0.3039-0.35890.10671.14-00.9949-0.1977-0.06130.81360.10560.865632.541-40.27421.6716
21.3657-0.08160.62922.5281-1.96451.72720.1904-0.1988-0.1090.5076-0.1873-0.0537-0.32390.17130.00290.6494-0.17570.00110.43410.060.656422.0248-33.1085-0.0106
31.17840.3617-0.1811.6976-1.89752.15420.16310.1136-0.0140.81360.70570.7374-0.6442-0.98570.24120.8010.02780.26820.75710.23040.97954.5268-27.30050.4911
41.92540.50771.11982.3903-0.71411.12230.0919-0.3085-0.00141.75440.57460.7559-1.1793-0.74420.371.30950.21310.43990.86490.25230.99025.1699-28.519113.596
50.88290.438-0.41311.86810.50983.8376-0.3850.6314-0.0908-0.27420.3906-0.1728-0.2120.7373-0.13860.9067-0.56990.04220.7079-0.01640.884213.8736-48.3548-2.6174
60.93260.0808-0.13290.7346-0.43750.2156-0.31610.7887-0.0826-1.34610.0451-0.35921.8435-0.0708-0.30531.861-0.35110.08110.5143-0.18920.624918.3007-35.1812-30.841
70.5766-0.3532-0.52641.5117-1.1832.22590.03140.1454-0.24750.2420.2060.08420.1899-0.2109-0.00010.6881-0.09640.01180.50440.03840.633619.0186-17.0896-23.9937
81.58170.6707-1.22491.0012-0.70070.9663-0.15980.93280.2848-1.01440.11-0.0897-0.1584-0.1778-0.06610.9255-0.04830.05770.8980.11450.725125.5093-15.6287-39.4343
90.1661-0.37970.13420.7702-0.33050.14620.23350.0089-0.03070.2642-1.0871-0.27090.032-0.2896-0.69580.7755-0.07770.19120.98670.10730.882234.1263-33.6115-22.7019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 125 through 154 )
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 228 )
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 375 )
4X-RAY DIFFRACTION4chain 'A' and (resid 376 through 418 )
5X-RAY DIFFRACTION5chain 'A' and (resid 419 through 466 )
6X-RAY DIFFRACTION6chain 'B' and (resid 125 through 271 )
7X-RAY DIFFRACTION7chain 'B' and (resid 272 through 353 )
8X-RAY DIFFRACTION8chain 'B' and (resid 354 through 418 )
9X-RAY DIFFRACTION9chain 'B' and (resid 419 through 467 )

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