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- PDB-8u2o: Crystal Structure of Cdk-related protein kinase 6 (PK6) from Plas... -

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Basic information

Entry
Database: PDB / ID: 8u2o
TitleCrystal Structure of Cdk-related protein kinase 6 (PK6) from Plasmodium falciparum in complex with inhibitor TCMDC-123995
ComponentsProtein kinase 6
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Protein kinase 6 / inhibitor TCMDC-123995
Function / homology
Function and homology information


mediator complex / [RNA-polymerase]-subunit kinase / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / RNA polymerase II CTD heptapeptide repeat kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / 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-V3O / Cyclin-dependent kinase 2 homolog
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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 Cdk-related protein kinase 6 (PK6) from Plasmodium falciparum in complex with inhibitor TCMDC-123995
Authors: Lovell, S. / Liu, L. / Woodward, E.L. / Battaile, K.P. / DeRocher, A.
History
DepositionSep 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase 6
B: Protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,23712
Polymers71,9892
Non-polymers1,24810
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-68 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.977, 46.485, 111.278
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protein kinase 6


Mass: 35994.555 Da / Num. of mol.: 2 / Mutation: C44N, C53R, C222N, K237A, K86A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1337100 / Plasmid: PlfaA.01252.a.A13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IDW1

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Non-polymers , 5 types, 142 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-V3O / N-[(4P)-2-(4-chloroanilino)-4'-methyl[4,5'-bi-1,3-thiazol]-2'-yl]acetamide


Mass: 364.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13ClN4OS2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Index G5: 25% (w/v) PEG 3350, 0.1 M Tris pH 8.5, 0.2 M Lithium sulfate monohydrate. PlfaA.01252.a.A13.PW39218 at 15.9 mg/mL. His tag cleaved with 3C protease. 2mM TCMDC-123995 added prior to ...Details: Index G5: 25% (w/v) PEG 3350, 0.1 M Tris pH 8.5, 0.2 M Lithium sulfate monohydrate. PlfaA.01252.a.A13.PW39218 at 15.9 mg/mL. His tag cleaved with 3C protease. 2mM TCMDC-123995 added prior to crystallization. plate EWC2 well E12. Puck: PSL-1008, Cryo: 80% crystallant + 20% PEG200.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 6, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→46.49 Å / Num. obs: 36603 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.047 / Rrim(I) all: 0.116 / Χ2: 0.99 / Net I/σ(I): 9.1 / Num. measured all: 216398
Reflection shellResolution: 2.15→2.22 Å / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.963 / Num. measured all: 19305 / Num. unique obs: 3157 / CC1/2: 0.719 / Rpim(I) all: 0.424 / Rrim(I) all: 1.054 / Χ2: 1.01 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5057: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→38.65 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2815 1825 4.99 %
Rwork0.2181 --
obs0.2212 36563 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 72 132 4788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094743
X-RAY DIFFRACTIONf_angle_d1.0286404
X-RAY DIFFRACTIONf_dihedral_angle_d13.3991776
X-RAY DIFFRACTIONf_chiral_restr0.055717
X-RAY DIFFRACTIONf_plane_restr0.011795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.35251360.29592678X-RAY DIFFRACTION100
2.21-2.270.32331500.27522615X-RAY DIFFRACTION100
2.27-2.350.33221400.24772640X-RAY DIFFRACTION100
2.35-2.430.34531500.25032652X-RAY DIFFRACTION100
2.43-2.530.30351380.23722670X-RAY DIFFRACTION100
2.53-2.640.27611460.24362632X-RAY DIFFRACTION100
2.64-2.780.34241200.25022692X-RAY DIFFRACTION100
2.78-2.960.29761460.24692648X-RAY DIFFRACTION100
2.96-3.180.31671370.24852676X-RAY DIFFRACTION100
3.18-3.50.32091290.22482697X-RAY DIFFRACTION100
3.5-4.010.27931490.20122658X-RAY DIFFRACTION100
4.01-5.050.22541310.17192722X-RAY DIFFRACTION99
5.05-38.650.24961530.20632758X-RAY DIFFRACTION99
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)
14.02712.08890.6951.14070.09881.8982-0.00590.5205-0.4271-0.04050.2515-0.15750.18220.2132-0.24180.46860.0397-0.04540.28630.01250.347617.84124.361735.5737
21.0130.0713-0.35111.3584-0.04763.44030.0379-0.05450.0083-0.13870.05140.11550.13760.081-0.08670.3852-0.0099-0.0440.23790.00480.30799.27051.467851.495
34.7739-0.74480.04682.52650.20564.73450.1338-0.3964-0.09580.0877-0.02340.2170.1889-0.3573-0.07850.4498-0.0591-0.00110.34020.02520.3209-0.5651-3.020466.3887
48.9631.40440.34994.42712.07832.2496-0.0524-0.0227-0.04280.05570.8205-0.4271-0.5030.1844-0.68470.59820.04160.02790.4388-0.01640.376613.7504-7.321910.1777
52.5456-0.06020.57780.71831.31564.2777-0.12930.03480.0665-0.04120.1034-0.0072-0.21690.15050.05420.4564-0.0125-0.01590.25310.06230.32065.9467-6.561715.5182
62.1113-0.13971.01333.0604-0.0193.1338-0.0875-0.2240.07850.12660.09580.3341-0.2639-0.5769-0.01510.35490.02290.05240.46990.01460.311-16.8108-0.18511.5612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 211 )
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 298 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 28 )
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 116 )
6X-RAY DIFFRACTION6chain 'B' and (resid 117 through 294 )

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