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Yorodumi- PDB-6yx2: Crystal structure of SHANK1 PDZ in complex with a peptide-small m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yx2 | ||||||||||||
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Title | Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid | ||||||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / protein protein interactions / PDZ domain hybrid structures / fragment-based drug discovery / beta-sheets / acylhydrazone | ||||||||||||
Function / homology | Function and homology information somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior ...somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior / habituation / regulation of AMPA receptor activity / ankyrin repeat binding / dendritic spine morphogenesis / Neurexins and neuroligins / adult behavior / positive regulation of dendritic spine development / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / excitatory synapse / long-term memory / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / SH3 domain binding / scaffold protein binding / protein-containing complex assembly / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / dendrite / protein-containing complex binding / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||||||||
Authors | Hegedus, Z. / Hobor, F. / Shoemark, D.K. / Celis, S. / Lian, L.J. / Trinh, C.H. / Sessions, R.B. / Edwards, T.A. / Wilson, A.J. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Chem Sci / Year: 2021 Title: Identification of beta-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation. Authors: Hegedus, Z. / Hobor, F. / Shoemark, D.K. / Celis, S. / Lian, L.Y. / Trinh, C.H. / Sessions, R.B. / Edwards, T.A. / Wilson, A.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yx2.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yx2.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yx2_validation.pdf.gz | 898.7 KB | Display | wwPDB validaton report |
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Full document | 6yx2_full_validation.pdf.gz | 900.1 KB | Display | |
Data in XML | 6yx2_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6yx2_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/6yx2 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/6yx2 | HTTPS FTP |
-Related structure data
Related structure data | 6ywzC 6yx0C 6yx1C 1q3oS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12341.283 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SHANK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y566 #2: Protein/peptide | Mass: 389.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.75 / Details: 0.1 M HEPES 7.75 PEG 400 40% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.618→65.64 Å / Num. obs: 33616 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.618→1.65 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1 / Num. unique obs: 8301 / CC1/2: 0.863 / Rpim(I) all: 0.522 / Rrim(I) all: 1.24 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q3O Resolution: 1.62→52.26 Å / SU ML: 0.2582 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7788 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→52.26 Å
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Refine LS restraints |
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LS refinement shell |
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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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