+Open data
-Basic information
Entry | Database: PDB / ID: 3rdh | ||||||
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Title | X-ray induced covalent inhibition of 14-3-3 | ||||||
Components | 14-3-3 protein zeta/delta | ||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / phosphoSer/Thr-mimetic agent / phosphoserine/threonine-recognition protein / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information Golgi reassembly / synaptic target recognition / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA ...Golgi reassembly / synaptic target recognition / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / tube formation / 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 / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / negative regulation of innate immune response / protein sequestering activity / hippocampal mossy fiber to CA3 synapse / regulation of ERK1 and ERK2 cascade / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / lung development / regulation of protein stability / melanosome / DNA-binding transcription factor binding / angiogenesis / vesicle / transmembrane transporter binding / blood microparticle / cadherin binding / protein domain specific binding / protein phosphorylation / 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 / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Horton, J.R. / Upadhyay, A.K. / Fu, H. / Cheng, X. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Discovery and structural characterization of a small molecule 14-3-3 protein-protein interaction inhibitor. Authors: Zhao, J. / Du, Y. / Horton, J.R. / Upadhyay, A.K. / Lou, B. / Bai, Y. / Zhang, X. / Du, L. / Li, M. / Wang, B. / Zhang, L. / Barbieri, J.T. / Khuri, F.R. / Cheng, X. / Fu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rdh.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rdh.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 3rdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/3rdh ftp://data.pdbj.org/pub/pdb/validation_reports/rd/3rdh | HTTPS FTP |
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-Related structure data
Related structure data | 2o02S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 28059.369 Da / Num. of mol.: 4 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-3RD / #3: Chemical | ChemComp-NI / #4: Water | ChemComp-HOH / | Nonpolymer details | X-RAY INDUCED COVALENT MODIFICATION OF LYSINE RESIDUE. N1 ATOM OF PYRIDOXAL-PHOSPHATE MOIETY OF ...X-RAY INDUCED COVALENT MODIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.21 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG3350, 100 mM Tris-HCl pH 8.5, 10 mM MgCl2, 1 mM NiCl2, 1% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97926 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→33.77 Å / Num. obs: 47706 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.39→2.48 Å / Redundancy: 4 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4785 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 2O02 Resolution: 2.39→33.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 301274.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.9059 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.39→33.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.48 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
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