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- PDB-9z8k: Crystal Structure of serine/threonine-protein kinase (AEK1) from ... -

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Basic information

Entry
Database: PDB / ID: 9z8k
TitleCrystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma brucei
Components(Serine/threonine-protein ...) x 2
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / AEK1
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / nuclear lumen / ciliary plasm / mitotic cytokinesis / protein phosphorylation / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
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
Serine/threonine-protein kinase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 brucei
Authors: Lovell, S. / Seibold, S. / Battaile, K.P.
History
DepositionNov 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase
B: Serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,69124
Polymers82,1882
Non-polymers1,50322
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-212 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.599, 89.098, 201.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-504-

SO4

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Components

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Serine/threonine-protein ... , 2 types, 2 molecules AB

#1: Protein Serine/threonine-protein kinase


Mass: 41133.816 Da / Num. of mol.: 1 / Fragment: residues 54-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb03.48O8.470, Tb927.3.2440 / Plasmid: TrbrA.01480.a.WW4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q582V7, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein Serine/threonine-protein kinase


Mass: 41053.836 Da / Num. of mol.: 1 / Fragment: residues 54-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb03.48O8.470, Tb927.3.2440 / Plasmid: TrbrA.01480.a.WW4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q582V7, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Non-polymers , 4 types, 172 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: IDX G2 (25% (w/v) PEG 3350, 0.1 M BIS-TRIS pH 5.5, 0.2 M lithium sulfate. TrbrA.01480.a.WW4.PS38793 at 13.5 mg/mL. The C-terminal tail ~60 residues was disordered in each subunit. Residue ...Details: IDX G2 (25% (w/v) PEG 3350, 0.1 M BIS-TRIS pH 5.5, 0.2 M lithium sulfate. TrbrA.01480.a.WW4.PS38793 at 13.5 mg/mL. The C-terminal tail ~60 residues was disordered in each subunit. Residue Ser 71 in subunit A contained a large amount of density near the OG atom. This was modeled as a phosphoserine (SEP) although this is not a predicted phosphorylation site. plate 20520 G2 drop 1, Puck: PSL-0604, Cryo: 80% crystallant + 20% glycerol

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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: Nov 1, 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: 2.05→43.3 Å / Num. obs: 49269 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.025 / Rrim(I) all: 0.092 / Χ2: 0.95 / Net I/σ(I): 16.4 / Num. measured all: 657586
Reflection shellResolution: 2.05→2.11 Å / % possible obs: 99.9 % / Redundancy: 13.9 % / Rmerge(I) obs: 1.617 / Num. measured all: 52967 / Num. unique obs: 3797 / CC1/2: 0.815 / Rpim(I) all: 0.447 / Rrim(I) all: 1.678 / Χ2: 0.92 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(2.0_5882: ???)refinement
Aimlessdata scaling
XDSdata reduction
MoRDaphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→43.3 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 2552 5.18 %
Rwork0.1946 --
obs0.1966 49253 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 71 150 4595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054542
X-RAY DIFFRACTIONf_angle_d0.6446160
X-RAY DIFFRACTIONf_dihedral_angle_d16.4941663
X-RAY DIFFRACTIONf_chiral_restr0.046670
X-RAY DIFFRACTIONf_plane_restr0.006773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.31931680.28122521X-RAY DIFFRACTION100
2.09-2.130.28971410.26292559X-RAY DIFFRACTION100
2.13-2.180.27561230.24122610X-RAY DIFFRACTION100
2.18-2.230.26011430.24132543X-RAY DIFFRACTION100
2.23-2.280.29881530.22952559X-RAY DIFFRACTION100
2.28-2.350.25941290.2242574X-RAY DIFFRACTION100
2.35-2.420.22981600.20712563X-RAY DIFFRACTION100
2.42-2.490.26361510.21192552X-RAY DIFFRACTION100
2.49-2.580.27771470.21032591X-RAY DIFFRACTION100
2.58-2.690.24561370.20342555X-RAY DIFFRACTION100
2.69-2.810.25591320.21732587X-RAY DIFFRACTION100
2.81-2.960.2431360.21472603X-RAY DIFFRACTION100
2.96-3.140.25411480.2142588X-RAY DIFFRACTION100
3.14-3.380.20581580.20842581X-RAY DIFFRACTION100
3.38-3.720.20271330.18132616X-RAY DIFFRACTION100
3.72-4.260.20981240.15882655X-RAY DIFFRACTION100
4.26-5.370.20411190.15332677X-RAY DIFFRACTION100
5.37-43.30.25541500.20972767X-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)
12.0260.8946-0.60091.188-0.41850.51630.0048-0.00290.1297-0.0848-0.03090.1199-0.0875-0.04140.02090.32760.0278-0.00530.37060.01110.35380.79916.719656.5629
23.3485-0.36511.07181.7302-0.65974.0297-0.03110.28990.1152-0.07660.03640.117-0.0315-0.2484-0.00080.2452-0.0320.0170.29320.05410.35310.592628.236441.1333
32.8176-1.42253.62538.6917-1.8556.1098-0.8478-0.51390.99850.02750.4235-0.2446-2.04970.62780.38260.8997-0.0956-0.05130.6472-0.06720.571625.456337.588474.3889
41.0081-0.316-1.67064.26421.3763.7364-0.2885-0.20310.50890.21960.1591-0.6094-0.35980.86410.17950.5442-0.1302-0.06640.5806-0.04230.503832.423929.387476.6402
59.36914.6186-0.70719.087-1.22264.2514-0.1925-0.41910.3033-0.5726-0.2758-0.6439-0.44250.680.3340.4424-0.08420.00260.57510.07480.377529.00226.887771.4719
65.6205-1.62670.15534.6568-0.48812.67160.0459-0.54080.33660.3184-0.0984-0.0573-0.29960.05360.05530.4061-0.06240.00030.51060.02860.283315.82216.950582.063
71.58952.7699-2.10486.1017-4.05563.23350.0569-0.4156-0.2970.4694-0.4153-0.773-0.86480.70410.45060.6541-0.0886-0.10790.96810.1830.552829.364714.887490.7064
82.0549-0.59360.66131.7479-1.5195.9653-0.0494-0.73-0.27890.2811-0.05910.07960.17420.03020.07880.4053-0.03680.04650.62250.15090.363916.4147.267489.0774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 202 )
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 348 )
3X-RAY DIFFRACTION3chain 'B' and (resid 53 through 80 )
4X-RAY DIFFRACTION4chain 'B' and (resid 81 through 111 )
5X-RAY DIFFRACTION5chain 'B' and (resid 112 through 138 )
6X-RAY DIFFRACTION6chain 'B' and (resid 139 through 202 )
7X-RAY DIFFRACTION7chain 'B' and (resid 203 through 248 )
8X-RAY DIFFRACTION8chain 'B' and (resid 249 through 347 )

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