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

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Basic information

Entry
Database: PDB / ID: 6fna
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


synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / tube formation / regulation of synapse maturation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA ...synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / tube formation / 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 / Interleukin-3, Interleukin-5 and GM-CSF signaling / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / regulation of ERK1 and ERK2 cascade / protein targeting / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / ERK1 and ERK2 cascade / negative regulation of TORC1 signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / lung development / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / regulation of protein stability / Negative regulation of NOTCH4 signaling / melanosome / intracellular protein localization / angiogenesis / protein phosphatase binding / blood microparticle / vesicle / DNA-binding transcription factor binding / transmembrane transporter binding / protein phosphorylation / cadherin binding / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / protein kinase binding / negative regulation of apoptotic process / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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-DWE / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 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 / struct_conn_type
Revision 1.3Jan 17, 2024Group: 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

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)55,55014
Polymers52,6342
Non-polymers2,91612
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-84 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.035, 102.888, 113.627
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 405 molecules

#2: Chemical ChemComp-DWE / [2-[2-oxidanylidene-2-[[3-[2-[2-[2-[3-oxidanylidene-3-[2-[3-[2-[2-[2-[[4-[2-(2-phosphonophenoxy)ethanoylamino]phenyl]carbonylamino]ethoxy]ethoxy]ethoxy]propanoylamino]ethylamino]propoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]amino]ethoxy]phenyl]phosphonic acid


Mass: 1133.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H66N6O20P2
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 393 / 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 Å3/Da / Density % sol: 69.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.18 M Magnesium chloride 0.09 M Sodium HEPES pH 7.5 10% (v/v) Glycerol 27% (v/v) Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.12→46.86 Å / Num. obs: 48277 / % possible obs: 99.8 % / Redundancy: 13.254 % / Biso Wilson estimate: 51.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.1 / Χ2: 1.066 / Net I/σ(I): 16.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.12-2.2513.2460.8222.9276180.8840.85598.9
2.25-2.4113.3860.4844.9872440.9620.503100
2.41-2.613.1950.2967.767660.9830.307100
2.6-2.8513.8540.17912.6462400.9940.186100
2.85-3.1813.1630.11319.256530.9960.118100
3.18-3.6713.5190.08428.4750680.9970.087100
3.67-4.4913.1250.07333.8842930.9970.076100
4.49-6.3212.7720.06934.4133810.9980.072100
6.32-46.8611.8350.07135.320140.9980.07499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.86 Å
Translation2.5 Å46.86 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NKX

3nkx


Resolution: 2.12→46.86 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.279 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1619 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.152
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 2411 5 %RANDOM
Rwork0.2018 ---
obs0.2035 45800 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.19 Å2 / Biso mean: 48.821 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å20 Å2
2--2.55 Å20 Å2
3----2.66 Å2
Refinement stepCycle: final / Resolution: 2.12→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3543 0 118 394 4055
Biso mean--54.23 59.63 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023711
X-RAY DIFFRACTIONr_bond_other_d0.0040.023357
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.9935002
X-RAY DIFFRACTIONr_angle_other_deg0.9953.0077764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0585454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63925.088171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3215637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1441522
X-RAY DIFFRACTIONr_chiral_restr0.0520.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
LS refinement shellResolution: 2.125→2.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 172 -
Rwork0.283 3266 -
all-3438 -
obs--97.53 %

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