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

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Basic information

Entry
Database: PDB / ID: 10sl
TitleCrystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with Hesperadin
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
Chem-H1N / MALONATE ION / Serine/threonine protein kinase, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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 Hesperadin
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionFeb 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)84,5945
Polymers83,4592
Non-polymers1,1353
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-44 kcal/mol
Surface area29240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.518, 86.518, 193.041
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-603-

HOH

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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-H1N / N-[2-OXO-3-((E)-PHENYL{[4-(PIPERIDIN-1-YLMETHYL)PHENYL]IMINO}METHYL)-2,6-DIHYDRO-1H-INDOL-5-YL]ETHANESULFONAMIDE / HESPERADIN


Mass: 516.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H32N4O3S / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Chemical ChemComp-MLI / MALONATE ION


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
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 Hespreadin solubilized in 3.0M ...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 Hespreadin solubilized in 3.0M Malonate, pH 5.0 which displaced the ATP. plate Liu-S-198, Puck: PSL-1705, 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: Jan 31, 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: 2.72→48.82 Å / Num. obs: 23234 / % possible obs: 99.9 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.032 / Rrim(I) all: 0.143 / Χ2: 1.19 / Net I/σ(I): 18.8 / Num. measured all: 466916
Reflection shellResolution: 2.72→2.79 Å / % possible obs: 100 % / Redundancy: 21.4 % / Rmerge(I) obs: 2.084 / Num. measured all: 36084 / Num. unique obs: 1690 / CC1/2: 0.899 / Rpim(I) all: 0.46 / Rrim(I) all: 2.134 / Χ2: 1.03 / Net I/σ(I) obs: 1.5

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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: 2.72→48.82 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1126 4.87 %
Rwork0.2231 --
obs0.2254 23100 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.72→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 81 11 5417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025545
X-RAY DIFFRACTIONf_angle_d0.5737521
X-RAY DIFFRACTIONf_dihedral_angle_d12.3472080
X-RAY DIFFRACTIONf_chiral_restr0.042797
X-RAY DIFFRACTIONf_plane_restr0.004981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.840.37841220.33212678X-RAY DIFFRACTION99
2.84-2.990.37741310.28522709X-RAY DIFFRACTION99
2.99-3.180.39561350.30882704X-RAY DIFFRACTION100
3.18-3.430.33091370.27962711X-RAY DIFFRACTION99
3.43-3.770.30121480.24232735X-RAY DIFFRACTION100
3.77-4.320.25061450.1972755X-RAY DIFFRACTION100
4.32-5.440.2311500.19132775X-RAY DIFFRACTION100
5.44-48.820.23081580.19862907X-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)
18.60023.63260.87992.71-0.62292.6053-0.72521.15150.1622-0.43910.5118-0.5590.61790.1450.08080.6839-0.1008-0.02090.76640.0850.783132.4139-40.2076-0.9471
22.00450.9736-0.89692.6738-3.1624.02450.09140.11920.0253-0.1598-0.3012-0.02620.41220.1370.2250.553-0.1199-0.04480.4087-0.06350.593428.1111-31.7886-1.1161
34.147-1.0512-0.56132.7432-1.58376.86060.1635-0.5405-0.17770.39830.20670.51260.159-0.5047-0.3170.5903-0.0420.07880.520.04030.740410.1741-34.48367.0254
48.1372.51412.07077.31210.11186.89640.24780.49940.81250.0185-0.1499-0.1932-0.6909-0.6956-0.07350.62430.05420.14810.52140.03540.761710.5529-19.6482-5.2608
53.3201-0.0341-0.02444.0926-0.85385.78740.0276-0.09730.20720.54120.41681.0529-0.3085-1.4509-0.43870.55380.03020.23120.74860.15190.9686-2.9694-29.23553.2235
67.8362-2.988-1.51917.61140.9374.1159-0.2296-0.7826-0.4420.16720.5549-0.0896-0.74180.4871-0.31330.7433-0.1513-0.08240.65840.1530.543620.9449-44.87417.7466
70.8021-1.54942.07252.8075-3.85345.3-0.0890.0302-0.2044-0.75050.6140.71250.9809-0.3746-0.31280.9382-0.31160.0090.72870.02980.88888.4185-48.7791-9.2674
82.6021.5831-1.08342.1795-0.02040.7601-0.3520.1658-0.3562-0.36730.16390.0361.2123-0.05050.14361.4641-0.1390.02760.5131-0.07050.740917.742-40.1581-28.9338
93.3335-1.3229-1.74544.01550.82435.4476-0.01770.2136-0.4997-0.55160.09020.29041.0217-0.44270.00050.9188-0.1747-0.0750.3879-0.04720.670915.8137-24.573-33.3899
106.97920.2349-0.62783.40670.35165.61150.0191-0.0458-0.23460.1629-0.07790.37240.069-0.11540.09210.6309-0.03450.00610.32970.00460.556120.5442-16.2896-24.7256
111.51860.1881-0.06433.8426-1.03224.80650.00930.23110.1046-0.0469-0.0725-0.0657-0.1693-0.13070.01830.6132-0.08120.05170.39030.00270.619327.3813-11.8688-32.1364
120.0847-0.1662-0.54990.8670.87392.7708-0.0853-0.0119-0.0964-0.2428-0.1858-0.20430.45570.4960.28790.8075-0.0670.12550.54370.01040.772132.8538-34.8856-31.2326
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 271 )
4X-RAY DIFFRACTION4chain 'A' and (resid 272 through 317 )
5X-RAY DIFFRACTION5chain 'A' and (resid 318 through 404 )
6X-RAY DIFFRACTION6chain 'A' and (resid 405 through 429 )
7X-RAY DIFFRACTION7chain 'A' and (resid 430 through 467 )
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 228 )
9X-RAY DIFFRACTION9chain 'B' and (resid 229 through 293 )
10X-RAY DIFFRACTION10chain 'B' and (resid 294 through 334 )
11X-RAY DIFFRACTION11chain 'B' and (resid 335 through 404 )
12X-RAY DIFFRACTION12chain 'B' and (resid 405 through 468 )

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