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- PDB-4iaa: Crystal structure of Ser/Thr kinase Pim1 in complex with thioridazine -

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Basic information

Entry
Database: PDB / ID: 4iaa
TitleCrystal structure of Ser/Thr kinase Pim1 in complex with thioridazine
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / pim1 kinase/oncogene/thioridazine / Ser/Thr kinase / thioridazine
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 ...Serine/threonine-protein kinase pim-1/2/3 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-RTZ / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZhang, W. / Wan, X. / Li, W. / Xie, Y. / Huang, N.
CitationJournal: To be Published
Title: Crystal structure of Ser/Thr kinase Pim1 in complex with thioridazine
Authors: Zhang, W. / Wan, X. / Li, W. / Xie, Y. / Huang, N.
History
DepositionDec 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Serine/threonine-protein kinase pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6632
Polymers33,2931
Non-polymers3711
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.817, 98.817, 80.507
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Serine/threonine-protein kinase pim-1


Mass: 33292.719 Da / Num. of mol.: 1 / Fragment: UNP residues 120-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-RTZ / 10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine


Mass: 370.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.4M sodium/potassium tartrate, pH 7.9, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. all: 10535 / Num. obs: 10412 / % possible obs: 99.2 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→19.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / ESU R: 0.843 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 493 4.7 %RANDOM
Rwork0.1846 ---
obs0.1868 10398 98.84 %-
all-10480 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.19 Å2 / Biso mean: 59.4077 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 25 5 2258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192305
X-RAY DIFFRACTIONr_bond_other_d00.022169
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9613128
X-RAY DIFFRACTIONr_angle_other_deg3.85134978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.695270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42623.136118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.58115379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7861521
X-RAY DIFFRACTIONr_chiral_restr0.0790.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212578
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02565
LS refinement shellResolution: 2.853→2.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 31 -
Rwork0.426 681 -
all-712 -
obs--93.93 %

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