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- PDB-9cmz: Crystal Structure of Cdk-related protein kinase 6 (PK6) from Plas... -

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Basic information

Entry
Database: PDB / ID: 9cmz
TitleCrystal Structure of Cdk-related protein kinase 6 (PK6) from Plasmodium falciparum in complex with inhibitor KG2-051
ComponentsProtein kinase 6
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Protein kinase 6 / Plasmodium falciparum / inhibitor
Function / homology
Function and homology information


mediator complex / [RNA-polymerase]-subunit kinase / cyclin-dependent kinase / cyclin-dependent protein serine/threonine 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
: / Cyclin-dependent kinase 2 homolog
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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 KG2-051
Authors: Seibold, S. / Lovell, S. / Mian, M.R.
History
DepositionJul 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: 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
C: Protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,48013
Polymers107,5423
Non-polymers1,93710
Water46826
1
A: Protein kinase 6
B: Protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,03410
Polymers71,6952
Non-polymers1,3398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4463
Polymers35,8471
Non-polymers5992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.539, 99.428, 78.148
Angle α, β, γ (deg.)90.00, 100.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein kinase 6


Mass: 35847.383 Da / Num. of mol.: 3 / 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, cyclin-dependent kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-A1AZE / (4-{[5-chloro-4-(5-chlorothiophen-2-yl)pyrimidin-2-yl]amino}phenyl)[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone


Mass: 502.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H25Cl2N5OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Berkeley F7: 20% (w/v) PEG MME 5000, 100 mM Tris pH 8.5, 200 mM lithium sulfate. PlfaA.01252.a.A13.PW39218 at 15.9 mg/mL. His tag cleaved with 3C protease. 2mM KG2-051 added prior to ...Details: Berkeley F7: 20% (w/v) PEG MME 5000, 100 mM Tris pH 8.5, 200 mM lithium sulfate. PlfaA.01252.a.A13.PW39218 at 15.9 mg/mL. His tag cleaved with 3C protease. 2mM KG2-051 added prior to crystallization. plate SS CloverBook4_pg5, Cryo: 80% crystallant + 20% PEG200.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: May 30, 2024
RadiationMonochromator: HELIOS MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→44.4 Å / Num. obs: 42580 / % possible obs: 99.3 % / Redundancy: 11.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.037 / Rrim(I) all: 0.127 / Χ2: 1.13 / Net I/σ(I): 18.8 / Num. measured all: 494144
Reflection shellResolution: 2.45→2.54 Å / % possible obs: 99.6 % / Redundancy: 10.3 % / Rmerge(I) obs: 1.894 / Num. measured all: 45821 / Num. unique obs: 4470 / CC1/2: 0.698 / Rpim(I) all: 0.602 / Rrim(I) all: 1.99 / Χ2: 0.93 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIXdev_5383refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→34.66 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 2094 4.93 %
Rwork0.2196 --
obs0.2214 42504 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6682 0 118 26 6826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096940
X-RAY DIFFRACTIONf_angle_d0.9739390
X-RAY DIFFRACTIONf_dihedral_angle_d19.2822552
X-RAY DIFFRACTIONf_chiral_restr0.0531068
X-RAY DIFFRACTIONf_plane_restr0.0071157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.41831420.35112697X-RAY DIFFRACTION99
2.51-2.570.38261300.31812687X-RAY DIFFRACTION99
2.57-2.640.381370.31132695X-RAY DIFFRACTION99
2.64-2.720.37811260.32962667X-RAY DIFFRACTION99
2.72-2.80.36711770.29252663X-RAY DIFFRACTION99
2.8-2.90.34151360.29352669X-RAY DIFFRACTION99
2.9-3.020.38481260.28912698X-RAY DIFFRACTION99
3.02-3.160.32271420.27112659X-RAY DIFFRACTION99
3.16-3.320.26281440.25792690X-RAY DIFFRACTION99
3.32-3.530.30881450.23242662X-RAY DIFFRACTION98
3.53-3.810.25361630.19742672X-RAY DIFFRACTION99
3.81-4.190.21851290.18632694X-RAY DIFFRACTION99
4.19-4.790.16951150.15122741X-RAY DIFFRACTION100
4.79-6.030.20991350.18662759X-RAY DIFFRACTION100
6.03-34.660.19711470.19612757X-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)
13.94860.4671-0.29421.5728-0.83353.40640.07510.6192-0.1472-0.1482-0.01240.10980.15630.5135-0.11450.40120.1202-0.08520.952-0.15190.4649-1.3501-4.8519-43.7766
23.9760.6929-1.27692.73480.0974.71130.17830.3597-0.15680.020.0173-0.1391-0.19160.9648-0.12540.37720.0906-0.05010.9761-0.00860.36785.421-4.1253-28.7718
34.6294-0.2662-1.24813.92920.76124.34570.37071.07450.6032-0.54570.16440.0282-0.57380.4243-0.53410.6813-0.1414-0.10320.97240.05910.4097.287711.3484-24.8966
43.05050.41411.10731.80111.38775.20340.2222-0.25810.24920.1489-0.1269-0.1256-0.19440.603-0.08570.43950.0323-0.00490.79850.00070.34954.913.9643-12.5065
53.63792.2817-0.01111.86441.06383.1633-0.1865-0.05170.1974-0.2913-0.13860.2009-0.0531-0.29630.40580.35240.2171-0.0681.0848-0.00880.43815.93845.6863-64.783
65.32420.0460.7221.4212-1.22012.4989-0.1523-0.19930.15570.01930.1990.0393-0.1859-0.7473-0.0230.36550.1318-0.01880.6573-0.12070.342228.85116.7891-56.4864
71.9868-1.4989-0.04292.1406-0.43021.6231-0.2642-0.1843-0.3207-0.02490.28840.31220.3113-0.1904-0.1160.25970.0505-0.01910.4951-0.01660.460140.7365-3.7375-52.5126
84.1487-1.0031.36212.2644-0.34644.6334-0.2331-0.51080.00970.2160.0609-0.2385-0.11790.49670.21220.28840.0428-0.07050.6388-0.06240.432451.5149-1.3994-49.1976
93.6773-0.9256-0.64551.8519-0.85392.53970.11480.46460.2241-0.2488-0.0893-0.2769-0.03760.3090.0040.76490.0510.09890.44570.07170.545848.73484.4365-11.0302
102.0418-0.3075-1.35393.2588-1.48254.92840.1369-0.1285-0.0836-0.38380.0207-0.17660.31720.4332-0.10350.58550.00520.11270.3231-0.09130.606144.0864-16.8922.1444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 173 )
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 194 )
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 294 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 51 )
6X-RAY DIFFRACTION6chain 'B' and (resid 52 through 174 )
7X-RAY DIFFRACTION7chain 'B' and (resid 175 through 211 )
8X-RAY DIFFRACTION8chain 'B' and (resid 212 through 296 )
9X-RAY DIFFRACTION9chain 'C' and (resid 4 through 164 )
10X-RAY DIFFRACTION10chain 'C' and (resid 165 through 295 )

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