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- PDB-3nfl: Crystal structure of the PTPN4 PDZ domain complexed with the C-te... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nfl | ||||||
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Title | Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit | ||||||
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![]() | PROTEIN BINDING / PDZ-PDZ-binding site complex | ||||||
Function / homology | ![]() excitatory chemical synaptic transmission / directional locomotion / Toll Like Receptor 4 (TLR4) Cascade / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / sleep / activation of cysteine-type endopeptidase activity / regulation of monoatomic cation transmembrane transport / glutamate receptor signaling pathway ...excitatory chemical synaptic transmission / directional locomotion / Toll Like Receptor 4 (TLR4) Cascade / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / sleep / activation of cysteine-type endopeptidase activity / regulation of monoatomic cation transmembrane transport / glutamate receptor signaling pathway / NMDA glutamate receptor activity / Assembly and cell surface presentation of NMDA receptors / Interleukin-37 signaling / Neurexins and neuroligins / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / calcium ion transmembrane import into cytosol / dopamine metabolic process / Negative regulation of NMDA receptor-mediated neuronal transmission / startle response / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / positive regulation of excitatory postsynaptic potential / Long-term potentiation / non-membrane spanning protein tyrosine phosphatase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / sensory perception of pain / response to amphetamine / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / protein dephosphorylation / positive regulation of synaptic transmission, glutamatergic / protein-tyrosine-phosphatase / neurogenesis / synaptic membrane / protein tyrosine phosphatase activity / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / long-term synaptic potentiation / postsynaptic density membrane / protein catabolic process / visual learning / regulation of synaptic plasticity / cytoplasmic vesicle membrane / negative regulation of protein catabolic process / brain development / cytoplasmic side of plasma membrane / memory / response to wounding / synaptic vesicle / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / response to ethanol / dendritic spine / postsynaptic density / learning or memory / cytoskeleton / response to xenobiotic stimulus / positive regulation of apoptotic process / glutamatergic synapse / endoplasmic reticulum membrane / cell surface / zinc ion binding / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Babault, N. / Cordier, F. / Lafage, M. / Cockburn, J. / Haouz, A. / Rey, F.A. / Delepierre, M. / Buc, H. / Lafon, M. / Wolff, N. | ||||||
![]() | ![]() Title: Peptides Targeting the PDZ Domain of PTPN4 Are Efficient Inducers of Glioblastoma Cell Death. Authors: Babault, N. / Cordier, F. / Lafage, M. / Cockburn, J. / Haouz, A. / Prehaud, C. / Rey, F.A. / Delepierre, M. / Buc, H. / Lafon, M. / Wolff, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.1 KB | Display | ![]() |
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PDB format | ![]() | 133.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.5 KB | Display | ![]() |
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Full document | ![]() | 471.5 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nfkC ![]() 2vphS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11694.363 Da / Num. of mol.: 4 / Fragment: PDZ domain (UNP residues 499-604) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1913.204 Da / Num. of mol.: 4 / Fragment: UNP residues 1449-1464 / Source method: obtained synthetically Details: NR2A16 peptide has been chemically synthetized. The sequence ocuurs naturally in Homo sapiens (Human) Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 24% PEG 4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2009 |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) Dynamically bendable mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→95.45 Å / Num. all: 40560 / Num. obs: 38978 / % possible obs: 96.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.91→2.01 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2 / Num. unique all: 4287 / % possible all: 74.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VPH Resolution: 1.91→49.88 Å / Cor.coef. Fo:Fc: 0.9235 / Cor.coef. Fo:Fc free: 0.9025 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 54.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.387 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→49.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.96 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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