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- PDB-4ijp: Crystal Structure of Human PRPF4B kinase domain in complex with 4... -

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Basic information

Entry
Database: PDB / ID: 4ijp
TitleCrystal Structure of Human PRPF4B kinase domain in complex with 4-{5-[(2-Chloro-pyridin-4-ylmethyl)-carbamoyl]-thiophen-2-yl}-benzo[b]thiophene-2-carboxylic acid amine
ComponentsSerine/threonine-protein kinase PRP4 homolog
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


mRNA cis splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / chromosome / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / protein phosphorylation ...mRNA cis splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / chromosome / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Serine/threonine-protein PRP4, catalytic domain / 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 domain profile. ...Serine/threonine-protein PRP4, catalytic domain / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-1EH / Serine/threonine-protein kinase PRP4 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMechin, I. / Haas, K. / Chen, X. / Zhang, Y. / McLean, L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Evaluation of Cancer Dependence and Druggability of PRP4 Kinase Using Cellular, Biochemical, and Structural Approaches.
Authors: Gao, Q. / Mechin, I. / Kothari, N. / Guo, Z. / Deng, G. / Haas, K. / McManus, J. / Hoffmann, D. / Wang, A. / Wiederschain, D. / Rocnik, J. / Czechtizky, W. / Chen, X. / McLean, L. / Arlt, H. ...Authors: Gao, Q. / Mechin, I. / Kothari, N. / Guo, Z. / Deng, G. / Haas, K. / McManus, J. / Hoffmann, D. / Wang, A. / Wiederschain, D. / Rocnik, J. / Czechtizky, W. / Chen, X. / McLean, L. / Arlt, H. / Harper, D. / Liu, F. / Majid, T. / Patel, V. / Lengauer, C. / Garcia-Echeverria, C. / Zhang, B. / Cheng, H. / Dorsch, M. / Huang, S.M.
History
DepositionDec 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PRP4 homolog
B: Serine/threonine-protein kinase PRP4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,29910
Polymers83,8672
Non-polymers1,4328
Water3,117173
1
A: Serine/threonine-protein kinase PRP4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7466
Polymers41,9331
Non-polymers8125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase PRP4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5544
Polymers41,9331
Non-polymers6203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.140, 52.540, 79.130
Angle α, β, γ (deg.)102.560, 105.250, 92.290
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serine/threonine-protein kinase PRP4 homolog / PRP4 kinase / PRP4 pre-mRNA-processing factor 4 homolog


Mass: 41933.469 Da / Num. of mol.: 2 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0536, PRP4, PRP4H, PRP4K, PRPF4B / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q13523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-1EH / 4-(5-{[(2-chloropyridin-4-yl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide


Mass: 427.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H14ClN3O2S2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M ammonium sulfate, 20-30% PEG 3350 and 0.1M HEPES pH7.0 5 mM compound final concentration added to cryo-protectant solution for soaking of apo crystals, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 36692 / % possible obs: 98.4 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.051 / Χ2: 1.037 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.332.30.42736361.009197.5
2.33-2.422.30.33236571.059197.8
2.42-2.532.30.2536301.043197.8
2.53-2.672.30.17836841.026198.1
2.67-2.832.30.12736311.041198.1
2.83-3.052.30.09337011.045198.4
3.05-3.362.30.05936551.055198.7
3.36-3.852.30.03636831.032198.8
3.85-4.852.30.02837101.056199.2
4.85-502.30.02737051.008199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.9.1refinement
PDB_EXTRACT3.11data extraction
BUSTER2.9.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→47.61 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 1832 4.99 %RANDOM
Rwork0.2496 ---
obs0.2504 36691 98.27 %-
Displacement parametersBiso max: 213.64 Å2 / Biso mean: 51.2369 Å2 / Biso min: 22.48 Å2
Baniso -1Baniso -2Baniso -3
1-3.4387 Å26.8618 Å22.5407 Å2
2--5.6 Å2-12.5625 Å2
3----9.0387 Å2
Refine analyzeLuzzati coordinate error obs: 0.401 Å
Refinement stepCycle: LAST / Resolution: 2.25→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 86 173 5699
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2039SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes153HARMONIC2
X-RAY DIFFRACTIONt_gen_planes794HARMONIC5
X-RAY DIFFRACTIONt_it5582HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion697SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6513SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5644HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7607HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion1.59
X-RAY DIFFRACTIONt_other_torsion19.76
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.263 159 5.43 %
Rwork0.2734 2771 -
all0.2728 2930 -
obs--98.27 %

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