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- PDB-10ju: Crystal Structure of serine/threonine-protein kinase (AEK1) T376D... -

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Basic information

Entry
Database: PDB / ID: 10ju
TitleCrystal Structure of serine/threonine-protein kinase (AEK1) T376D, S395D Mutant from Trypanosoma brucei (AMP-PNP)
Components(Serine/threonine-protein kinase, putative) 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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) T376D, S395D Mutant from Trypanosoma brucei (AMP-PNP)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionJan 22, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,83514
Polymers82,2722
Non-polymers1,56312
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-106 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.538, 88.475, 201.132
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-506-

SO4

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Components

#1: Protein Serine/threonine-protein kinase, putative


Mass: 41175.809 Da / Num. of mol.: 1 / Fragment: residues 54-406 / Mutation: T376D, S395D
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.WW42 / 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, putative


Mass: 41095.828 Da / Num. of mol.: 1 / Fragment: residues 54-406 / Mutation: T376D, S395D
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.WW42 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q582V7, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Index F6 0.2M Ammonium sulfate 0.1M Bis-Tris pH 5.5 25% PEG 3350. 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 ...Details: Index F6 0.2M Ammonium sulfate 0.1M Bis-Tris pH 5.5 25% PEG 3350. 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. 2mM AMP-PNP and 2mM MgCl2 added prior to crystallization. Prominent AMP-PNP density in subunit B but disorder in the phosphate portion. plate 20522 F6 drop 2, Puck: PSL-0904, 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: 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: 2.15→44.24 Å / Num. obs: 42374 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.023 / Rrim(I) all: 0.082 / Χ2: 0.97 / Net I/σ(I): 17.2 / Num. measured all: 564111
Reflection shellResolution: 2.15→2.22 Å / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 1.693 / Num. measured all: 49777 / Num. unique obs: 3628 / CC1/2: 0.747 / Rpim(I) all: 0.473 / Rrim(I) all: 1.758 / Χ2: 0.97 / 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: 2.15→44.24 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 2230 5.26 %
Rwork0.2186 --
obs0.2202 42358 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 86 88 4278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054283
X-RAY DIFFRACTIONf_angle_d0.6415827
X-RAY DIFFRACTIONf_dihedral_angle_d15.3491542
X-RAY DIFFRACTIONf_chiral_restr0.047642
X-RAY DIFFRACTIONf_plane_restr0.006723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.33041260.28022447X-RAY DIFFRACTION100
2.2-2.250.29911410.27832481X-RAY DIFFRACTION100
2.25-2.30.36481560.27192443X-RAY DIFFRACTION100
2.3-2.370.35621390.27592510X-RAY DIFFRACTION100
2.37-2.440.34081550.26152445X-RAY DIFFRACTION100
2.44-2.510.25151410.23392482X-RAY DIFFRACTION100
2.51-2.60.25771280.23172502X-RAY DIFFRACTION100
2.6-2.710.24611360.2272494X-RAY DIFFRACTION100
2.71-2.830.25351340.23542497X-RAY DIFFRACTION100
2.83-2.980.33111530.2652487X-RAY DIFFRACTION100
2.98-3.170.28241280.23972505X-RAY DIFFRACTION100
3.17-3.410.25531260.23142534X-RAY DIFFRACTION100
3.41-3.760.241410.21672511X-RAY DIFFRACTION100
3.76-4.30.21891720.1882512X-RAY DIFFRACTION100
4.3-5.410.19641290.18512581X-RAY DIFFRACTION100
5.42-44.240.25811250.21752697X-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)
11.99350.761-0.64342.3302-0.82661.2119-0.0369-0.0655-0.0228-0.1137-0.07980.1168-0.0816-0.05160.09530.3710.0405-0.03110.4270.00090.4113-42.9949-28.6008-43.3098
23.9262-0.07460.92281.6442-1.14934.6711-0.01870.38910.0977-0.13020.14510.222-0.0125-0.372-0.110.3013-0.0320.00770.35770.07640.4149-33.0389-16.9815-58.4112
31.99370.0760.39485.4804-0.8444.6102-0.25310.55270.38940.17550.0247-0.7326-0.87350.39920.20060.7131-0.1221-0.07570.52480.1030.591-18.2609-13.2466-27.8651
42.1597-0.54070.78821.5323-1.54255.4402-0.1296-0.4917-0.11790.3021-0.12170.02860.01780.10890.23990.443-0.0390.03620.64370.07240.4213-25.4363-33.4134-13.763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 347 )
3X-RAY DIFFRACTION3chain 'B' and (resid 53 through 145 )
4X-RAY DIFFRACTION4chain 'B' and (resid 146 through 346 )

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