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- PDB-10bl: Crystal Structure of serine/threonine-protein kinase (AEK1) from ... -

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Basic information

Entry
Database: PDB / ID: 10bl
TitleCrystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex ADP
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-5'-DIPHOSPHATE / MALONATE ION / Serine/threonine protein kinase, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 ADP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionJan 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 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)84,6818
Polymers83,6182
Non-polymers1,0636
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-77 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.173, 86.173, 192.761
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: 41809.246 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Grid Salt Screen, C12: 3.40M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. 4mM ATP and 4mM MgCl2 added to the protein prior to crystallization but only ADP was bound. ...Details: Grid Salt Screen, C12: 3.40M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. 4mM ATP and 4mM MgCl2 added to the protein prior to crystallization but only ADP was bound. several Ser residues displayed electron density consistent with phosphorylation. plate 20528 C12, Puck: PSL-0916, Cryo: 2.5M LiSO4

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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: Dec 13, 2025
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: 2.6→48.69 Å / Num. obs: 26306 / % possible obs: 100 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.031 / Rrim(I) all: 0.14 / Χ2: 1.25 / Net I/σ(I): 20.3 / Num. measured all: 524559
Reflection shellResolution: 2.6→2.67 Å / % possible obs: 100 % / Redundancy: 19.4 % / Rmerge(I) obs: 2.509 / Num. measured all: 37252 / Num. unique obs: 1918 / CC1/2: 0.792 / Rpim(I) all: 0.581 / Rrim(I) all: 2.576 / Χ2: 1.01 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5904: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.69 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 1341 5.12 %
Rwork0.2146 --
obs0.2172 26170 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5340 0 64 5 5409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085536
X-RAY DIFFRACTIONf_angle_d1.0117518
X-RAY DIFFRACTIONf_dihedral_angle_d15.0112035
X-RAY DIFFRACTIONf_chiral_restr0.052806
X-RAY DIFFRACTIONf_plane_restr0.007956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.40971410.36432452X-RAY DIFFRACTION100
2.69-2.80.37081240.32522419X-RAY DIFFRACTION100
2.8-2.930.31841540.28792415X-RAY DIFFRACTION99
2.93-3.080.32541340.27492461X-RAY DIFFRACTION100
3.08-3.280.34621440.29752417X-RAY DIFFRACTION100
3.28-3.530.33791190.23942472X-RAY DIFFRACTION99
3.53-3.880.27481180.22452489X-RAY DIFFRACTION100
3.88-4.440.22271400.17682505X-RAY DIFFRACTION100
4.45-5.60.20741220.18152535X-RAY DIFFRACTION100
5.6-48.690.24431450.18212664X-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)
17.42332.463-0.34116.87460.91854.3432-0.28861.62970.3908-0.91120.37410.66980.75340.17880.20660.8512-0.1031-0.14350.8250.16290.788431.6605-39.8721-1.6422
22.54680.5626-0.65571.5627-2.37583.37690.0356-0.0995-0.00610.0246-0.1337-0.0761-0.0940.18230.11790.6469-0.1353-0.06150.4838-0.01660.621728.0468-31.7298-1.2039
35.0678-1.9629-0.59333.0884-0.7734.8746-0.3839-0.1422-0.66320.45530.7060.53510.3987-0.9745-0.33530.8468-0.10690.03420.720.15210.79039.2077-43.26276.4373
43.4691-0.9614-0.21293.4446-1.81584.98170.1015-0.18370.23450.06070.0344-0.3197-0.3728-0.4778-0.16990.76040.00820.11430.532-0.0310.769112.6268-24.96144.3912
58.8321.15050.10922.67061.86867.73540.52870.20320.0226-0.14580.03160.3202-0.8294-1.6743-0.5460.56660.15130.08520.86510.04780.71754.38-23.803-9.4163
62.59180.1193-0.17913.4125-0.74116.2048-0.09420.0480.10760.12730.55551.0715-0.5213-1.7564-0.46260.54850.00320.12541.02390.2310.9963-4.5055-30.2605-0.5262
74.8974-3.08170.32167.7446-0.99961.65050.0868-0.79050.08661.21290.37090.765-0.5171-0.7261-0.47971.09970.08060.24570.8220.0660.74387.4697-31.390917.6033
80.13840.1402-0.38541.4256-1.64832.26670.01660.08760.1241-0.3113-0.0176-0.03620.33250.14360.02870.9128-0.27250.04750.8436-0.07270.754114.1782-49.3619-2.3273
94.21341.4489-1.0031.29610.89072.0543-0.62670.2221-0.5639-0.30070.3419-0.091.23560.47240.30481.336-0.21730.07810.5666-0.00820.724714.73-43.308-26.2228
101.22631.3766-0.2184.2335-1.6134.0324-0.14890.2851-0.2706-0.57710.19430.06451.0399-0.3056-0.00460.7937-0.09370.01720.4221-0.03150.474418.7546-25.824-30.5449
111.31470.4358-0.20184.5693-1.06893.2098-0.09520.40490.1034-0.48660.0736-0.2901-0.09360.13320.02110.6389-0.07480.07890.60710.00620.600927.2258-15.3797-34.5633
121.7861-0.8617-1.28741.59371.3394.63120.00520.43410.02270.2138-0.53970.07711.08980.11330.60710.7755-0.06790.08460.75520.03470.733334.8548-35.4547-24.2828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 124 through 141 )
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 228 )
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 296 )
5X-RAY DIFFRACTION5chain 'A' and (resid 297 through 317 )
6X-RAY DIFFRACTION6chain 'A' and (resid 318 through 385 )
7X-RAY DIFFRACTION7chain 'A' and (resid 386 through 418 )
8X-RAY DIFFRACTION8chain 'A' and (resid 419 through 467 )
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 184 )
10X-RAY DIFFRACTION10chain 'B' and (resid 185 through 334 )
11X-RAY DIFFRACTION11chain 'B' and (resid 335 through 418 )
12X-RAY DIFFRACTION12chain 'B' and (resid 419 through 468 )

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