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- PDB-6cnh: Human PRPF4B in complex with Rebastinib -

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Basic information

Entry
Database: PDB / ID: 6cnh
TitleHuman PRPF4B in complex with Rebastinib
ComponentsSerine/threonine-protein kinase PRP4 homolog
KeywordsTRANSFERASE / Kinase / inhibitor / DCC2036 / Structural Genomics / Structural Genomics Consortium / SGC
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-919 / Serine/threonine-protein kinase PRP4 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGodoi, P.H.C. / Santiago, A.S. / Ramos, P.Z. / Fala, A.M. / Salmazo, A.P.T. / Counago, R.M. / Righetto, G.L. / Silva, P.N.B. / Gileadi, O. / Guimaraes, C.R.W. ...Godoi, P.H.C. / Santiago, A.S. / Ramos, P.Z. / Fala, A.M. / Salmazo, A.P.T. / Counago, R.M. / Righetto, G.L. / Silva, P.N.B. / Gileadi, O. / Guimaraes, C.R.W. / Massirer, K.B. / Arruda, P. / Elkins, J.M. / Edwards, A.M. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To be Published
Title: Crystal structure of the human PRPF4B in complex with Rebastinib
Authors: Godoi, P.H.C. / Santiago, A.S. / Ramos, P.Z. / Silva, P.N.B. / Righetto, G.L. / Guimaraes, C.R.W. / Massirer, K.B. / Arruda, P. / Elkins, J.M. / Edwards, A.M.
History
DepositionMar 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,8216
Polymers40,8831
Non-polymers9385
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-50 kcal/mol
Surface area15200 Å2
Unit cell
Length a, b, c (Å)85.169, 75.661, 68.075
Angle α, β, γ (deg.)90.00, 92.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1346-

HOH

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Components

#1: Protein Serine/threonine-protein kinase PRP4 homolog / PRPF4B / PRP4 kinase / PRP4 pre-mRNA-processing factor 4 homolog


Mass: 40883.387 Da / Num. of mol.: 1 / Fragment: UNP residues 657-1005
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF4B, KIAA0536, PRP4, PRP4H, PRP4K / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-919 / 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide / DCC-2036


Mass: 553.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28FN7O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG Smear High, 0.1 M N-(2-acetamido)iminodiacetic acid, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2→67.99 Å / Num. obs: 29242 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Rrim(I) all: 0.084 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2136 / Rpim(I) all: 0.344 / Rrim(I) all: 0.638 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IJP

4ijp


Resolution: 2→67.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.735 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20591 1351 4.6 %RANDOM
Rwork0.18221 ---
obs0.18341 27710 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0.6 Å2
2--1.24 Å20 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 2→67.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 61 147 2788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192721
X-RAY DIFFRACTIONr_bond_other_d0.0020.022554
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9693677
X-RAY DIFFRACTIONr_angle_other_deg0.9242.9875906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5825326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26224.16125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25315499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9481515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0013.9491293
X-RAY DIFFRACTIONr_mcbond_other1.9993.9481292
X-RAY DIFFRACTIONr_mcangle_it2.9945.9011612
X-RAY DIFFRACTIONr_mcangle_other2.9935.9021613
X-RAY DIFFRACTIONr_scbond_it2.5334.3191428
X-RAY DIFFRACTIONr_scbond_other2.5254.3011413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1146.3242038
X-RAY DIFFRACTIONr_long_range_B_refined5.97946.1343086
X-RAY DIFFRACTIONr_long_range_B_other5.91845.8323051
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 84 -
Rwork0.263 2048 -
obs--99.44 %

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