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- PDB-6pjj: Human PRPF4B bound to benzothiophene inhibitor 224 -

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Basic information

Entry
Database: PDB / ID: 6pjj
TitleHuman PRPF4B bound to benzothiophene inhibitor 224
ComponentsSerine/threonine-protein kinase PRP4 homolog
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / Serine/threonine-protein kinase PRP4 homolog / Structural Genomics Consortium / SGC / TRANSFERASE / splicing KINASE PRPF4B / 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-OCJ / PHOSPHATE ION / Serine/threonine-protein kinase PRP4 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsGodoi, P.H.C. / Santiago, A.S. / Fala, A.M. / Ramos, P.Z. / Sriranganadane, D. / Mascarello, A. / Segretti, N. / Azevedo, H. / Guimaraes, C.R.W. / Arruda, P. ...Godoi, P.H.C. / Santiago, A.S. / Fala, A.M. / Ramos, P.Z. / Sriranganadane, D. / Mascarello, A. / Segretti, N. / Azevedo, H. / Guimaraes, C.R.W. / Arruda, P. / Elkins, J.M. / Counago, R.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: to be published
Authors: Godoi, P.H.C. / Santiago, A.S. / Fala, A.M. / Ramos, P.Z. / Sriranganadane, D. / Mascarello, A. / Segretti, N. / Azevedo, H. / Guimaraes, C.R.W. / Arruda, P. / Elkins, J.M. / Counago, R.M.
History
DepositionJun 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
C: Serine/threonine-protein kinase PRP4 homolog
D: Serine/threonine-protein kinase PRP4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,74024
Polymers163,8534
Non-polymers2,88620
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)241.812, 241.812, 50.230
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 PRP4 homolog / PRP4 kinase / PRP4 pre-mRNA-processing factor 4 homolog


Mass: 40963.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF4B, KIAA0536, PRP4, PRP4H, PRP4K / Production host: Escherichia coli (E. coli)
References: UniProt: Q13523, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-OCJ / 4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide


Mass: 407.509 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H17N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.59 Å3/Da / Density % sol: 52.46 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.5, 0.1M Na/K phosphate, 15% PEG smear high, 10% etylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.4→120.91 Å / Num. obs: 66509 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.328 / Rpim(I) all: 0.075 / Rrim(I) all: 0.337 / Net I/σ(I): 8.4 / Num. measured all: 1335190 / Scaling rejects: 689
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.832 / Num. measured all: 90043 / Num. unique obs: 4383 / CC1/2: 0.815 / Rpim(I) all: 0.412 / Rrim(I) all: 1.878 / Net I/σ(I) obs: 2.2 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.53 Å79.15 Å
Translation3.53 Å79.15 Å

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CNH

6cnh


Resolution: 2.4→79.28 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.538 / SU ML: 0.175 / SU R Cruickshank DPI: 0.3352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.241
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 3265 4.9 %RANDOM
Rwork0.1903 ---
obs0.1928 63213 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 126.16 Å2 / Biso mean: 32.956 Å2 / Biso min: 8.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å2-0 Å2
2---0.11 Å20 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 2.4→79.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10260 0 184 226 10670
Biso mean--59.15 28.2 -
Num. residues----1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01310636
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710021
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.64114348
X-RAY DIFFRACTIONr_angle_other_deg1.1671.58323167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61651279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12422.599531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.342151917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7281554
X-RAY DIFFRACTIONr_chiral_restr0.0580.21357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022146
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 237 -
Rwork0.245 4572 -
all-4809 -
obs--99.96 %

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