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- PDB-8rpc: Crystal structure of PfCLK3 with TCMDC-135051 -

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Basic information

Entry
Database: PDB / ID: 8rpc
TitleCrystal structure of PfCLK3 with TCMDC-135051
Componentsnon-specific serine/threonine protein kinase
KeywordsSIGNALING PROTEIN / PfCLK3 Kinase domain
Function / homology
Function and homology information


mRNA cis splicing, via spliceosome / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Serine/threonine-protein PRP4, catalytic domain / : / 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
: / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.079 Å
AuthorsYelland, T.S. / Benazir, A. / Hole, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2024
Title: Targeting Pf CLK3 with Covalent Inhibitors: A Novel Strategy for Malaria Treatment.
Authors: Brettell, S.B. / Janha, O. / Begen, A. / Cann, G. / Sharma, S. / Olaniyan, N. / Yelland, T. / Hole, A.J. / Alam, B. / Mayville, E. / Gillespie, R. / Capper, M. / Fidock, D.A. / Milligan, G. ...Authors: Brettell, S.B. / Janha, O. / Begen, A. / Cann, G. / Sharma, S. / Olaniyan, N. / Yelland, T. / Hole, A.J. / Alam, B. / Mayville, E. / Gillespie, R. / Capper, M. / Fidock, D.A. / Milligan, G. / Clarke, D.J. / Tobin, A.B. / Jamieson, A.G.
History
DepositionJan 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5598
Polymers44,5831
Non-polymers9767
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-36 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.627, 128.801, 108.22
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-956-

HOH

21A-1035-

HOH

31A-1064-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein non-specific serine/threonine protein kinase


Mass: 44583.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: C923_03333 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: W7JM86, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 203 molecules

#2: Chemical ChemComp-A1H19 / 4-[2-[5-(diethylaminomethyl)-2-methoxy-phenyl]-1~{H}-pyrrolo[2,3-b]pyridin-4-yl]-2-propan-2-yl-benzoic acid


Mass: 471.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2 M ammonium sulphate 0.2 M potassium sodium tartrate tetrahydrate 0.1 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.079→64.4 Å / Num. obs: 22013 / % possible obs: 93 % / Redundancy: 6.22 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.993 / CC1/2 anomalous: -0.019 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.0656 / Rrim(I) all: 0.1687 / AbsDiff over sigma anomalous: 0.784 / Baniso tensor eigenvalue 1: 9.1936 Å2 / Baniso tensor eigenvalue 2: 0 Å2 / Baniso tensor eigenvalue 3: 27.0395 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.233 Å / Aniso diffraction limit 2: 2.045 Å / Aniso diffraction limit 3: 2.476 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 6.94 / Num. measured all: 136944 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91.7 / % possible ellipsoidal: 93 / % possible ellipsoidal anomalous: 91.7 / % possible spherical: 74.3 / % possible spherical anomalous: 72.6 / Redundancy anomalous: 3.3 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
6.433-64.46.370.084215.3570107010110011000.994-0.0470.03540.09150.69810099.910099.91003.6799.9
5.052-6.4336.420.10813.1470717071110111010.99-0.0270.0460.11760.7811001001001001003.49100
4.395-5.0526.870.103814.7475697569110111010.991-0.0190.04280.11240.80210099.910099.91003.6899.9
3.983-4.3957.010.111414.0477137713110111010.994-0.1190.04530.12040.78199.910099.910099.93.73100
3.687-3.9836.860.122512.6975477547110011000.9890.0430.05040.13260.80410099.910099.91003.6499.9
3.464-3.6876.570.144310.8172297229110111010.9870.0560.06080.15680.8681001001001001003.47100
3.288-3.4646.320.16469.2969556955110111010.9850.0250.07170.17980.85999.910099.910099.93.33100
3.14-3.2886.760.19188.0874287428109910990.98-0.0640.08010.20820.8381001001001001003.55100
3.017-3.146.950.24486.8176497649110111010.9710.0490.10.26470.81599.910099.910099.93.64100
2.91-3.0176.990.29845.5676987698110211020.9610.040.12090.32230.8041001001001001003.66100
2.817-2.917.060.35074.7977697769110011000.9510.0660.1420.37880.81199.910099.910099.93.69100
2.736-2.8177.10.40154.278157815110011000.945-0.0170.16140.43310.7411001001001001003.7100
2.662-2.7367.120.44683.7778357835110011000.948-0.0590.17920.48190.7751001001001001003.73100
2.596-2.6627.210.52723.279407940110211020.919-0.0890.21050.56810.7381001001001001003.74100
2.537-2.5966.870.60162.7175597559110111010.8830.0320.24730.65120.7691001001001001003.57100
2.48-2.5376.090.66782.2867036703110011000.8430.010.29430.73090.76799.199.199.199.199.13.1699.1
2.423-2.485.520.67382.0860806080110211020.8260.0360.31330.74470.76590.390.290.388.588.72.8790.2
2.353-2.4234.150.61751.9145664566109910990.767-0.020.33420.70570.73671.475.571.463.660.72.2175.5
2.261-2.3533.330.5541.836603660110011000.7620.0790.34530.65660.76357.564.657.543.238.61.8164.6
2.079-2.2612.860.60511.5431483148110211020.6380.0270.42180.74160.75960.865.560.81715.41.5565.5

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCJan 10, 2022data processing
Aimless0.7.8data scaling
autoPROC2.3.87data processing
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.079→22.35 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.266 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.281 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 957 -RANDOM
Rwork0.199 ---
obs0.2015 21980 74.2 %-
Displacement parametersBiso mean: 36.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.0184 Å20 Å20 Å2
2---4.0352 Å20 Å2
3---4.0169 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.079→22.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 64 196 3166
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083039HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.934087HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1098SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes510HARMONIC5
X-RAY DIFFRACTIONt_it3039HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion373SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2562SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion16.48
LS refinement shellResolution: 2.08→2.19 Å
RfactorNum. reflection% reflection
Rfree0.3034 23 -
Rwork0.2469 --
obs0.2495 468 11.36 %
Refinement TLS params.Origin x: -17.5596 Å / Origin y: -16.7876 Å / Origin z: -13.4169 Å
111213212223313233
T-0.0453 Å2-0.0025 Å2-0.0267 Å2--0.0914 Å2-0.021 Å2--0.0226 Å2
L0.7125 °2-0.109 °2-0.0581 °2-0.6909 °2-0.0688 °2--0.4364 °2
S0.0033 Å °-0.064 Å °-0.0023 Å °-0.064 Å °-0.0056 Å °-0.0049 Å °-0.0023 Å °-0.0049 Å °0.0023 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A338 - 694
2X-RAY DIFFRACTION1{ A|* }A701 - 1401

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