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- PDB-6fn9: Mono- and bivalent 14-3-3 inhibitors for characterizing supramole... -

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Basic information

Entry
Database: PDB / ID: 6fn9
TitleMono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-PEG interactions in proteins
Components14-3-3 protein zeta/delta
KeywordsPROTEIN BINDING / Inhibition / Mono- and bivalent 14-3-3 inhibitors / Supramolecular lysine-PEG
Function / homology
Function and homology information


Golgi reassembly / synaptic target recognition / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / tube formation / respiratory system process / regulation of synapse maturation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA ...Golgi reassembly / synaptic target recognition / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / tube formation / respiratory system process / regulation of synapse maturation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / negative regulation of innate immune response / protein sequestering activity / ERK1 and ERK2 cascade / regulation of ERK1 and ERK2 cascade / hippocampal mossy fiber to CA3 synapse / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / lung development / Negative regulation of NOTCH4 signaling / regulation of protein stability / protein localization / melanosome / angiogenesis / DNA-binding transcription factor binding / vesicle / blood microparticle / transmembrane transporter binding / cadherin binding / protein phosphorylation / protein domain specific binding / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / RNA binding / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein ...14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BENZOIC ACID / Chem-DW8 / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsBier, D. / Ottmann, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCRC1093 (Supramolecular Chemistry on Proteins) Germany
CitationJournal: Chemistry / Year: 2018
Title: Mono- and Bivalent 14-3-3 Inhibitors for Characterizing Supramolecular "Lysine Wrapping" of Oligoethylene Glycol (OEG) Moieties in Proteins.
Authors: Yilmaz, E. / Bier, D. / Guillory, X. / Briels, J. / Ruiz-Blanco, Y.B. / Sanchez-Garcia, E. / Ottmann, C. / Kaiser, M.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 19, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2538
Polymers52,6342
Non-polymers1,6206
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-85 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.940, 102.420, 113.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26316.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Chemical ChemComp-DW8 / [2-[2-oxidanylidene-2-[[3-[2-[2-[2-[3-oxidanylidene-3-(propylamino)propoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]amino]ethoxy]phenyl]phosphonic acid


Mass: 595.578 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H38N3O10P
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.09 M HEPES sodium salt pH 7.5 1.26 M tri-Sodium citrate 10 %(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.27→49.66 Å / Num. obs: 39544 / % possible obs: 100 % / Redundancy: 13.131 % / Biso Wilson estimate: 57.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.117 / Χ2: 1.031 / Net I/σ(I): 15.73 / Num. measured all: 519240 / Scaling rejects: 57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.27-2.4112.9781.9241.583095640464030.6672.003100
2.41-2.5813.8331.0982.7383203601660150.8561.14100
2.58-2.7813.3860.6084.7771709536053570.9460.63299.9
2.78-3.0513.1130.3028.8667805517151710.9860.314100
3.05-3.413.6060.14817.3361622453045290.9960.154100
3.4-3.9312.7060.08228.4252919416541650.9980.085100
3.93-4.813.1910.05340.445970348534850.9990.055100
4.8-6.7512.2550.05338.4733861276627630.9990.05699.9
6.75-49.6611.5070.03448.81190561666165610.03599.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.85 Å46.79 Å
Translation6.85 Å46.79 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→49.66 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2364 / WRfactor Rwork: 0.2124 / FOM work R set: 0.806 / SU B: 6.281 / SU ML: 0.149 / SU R Cruickshank DPI: 0.2171 / SU Rfree: 0.1869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 1975 5 %RANDOM
Rwork0.2308 ---
obs0.2321 37508 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.31 Å2 / Biso mean: 43.414 Å2 / Biso min: 33.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å20 Å2
2--2.71 Å2-0 Å2
3----2.98 Å2
Refinement stepCycle: final / Resolution: 2.27→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 108 120 3740
Biso mean--61.89 50.06 -
Num. residues----452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.023665
X-RAY DIFFRACTIONr_bond_other_d0.0030.022456
X-RAY DIFFRACTIONr_angle_refined_deg0.8381.9944934
X-RAY DIFFRACTIONr_angle_other_deg0.9013.0085993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.455447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31125.238168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32515640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0951521
X-RAY DIFFRACTIONr_chiral_restr0.0460.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
LS refinement shellResolution: 2.27→2.329 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 135 -
Rwork0.38 2515 -
all-2650 -
obs--99.96 %

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