+Open data
-Basic information
Entry | Database: PDB / ID: 6x48 | ||||||
---|---|---|---|---|---|---|---|
Title | Sortilin-Progranulin Interaction With Compound 17 | ||||||
Components | Sortilin | ||||||
Keywords | UNKNOWN FUNCTION / Protein Protein Interaction | ||||||
Function / homology | Function and homology information neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / Golgi to lysosome transport / myotube differentiation / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / retromer complex binding / maintenance of synapse structure / Golgi to endosome transport / nerve growth factor receptor activity ...neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / Golgi to lysosome transport / myotube differentiation / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / retromer complex binding / maintenance of synapse structure / Golgi to endosome transport / nerve growth factor receptor activity / vesicle organization / endosome transport via multivesicular body sorting pathway / nerve growth factor binding / protein targeting to lysosome / trans-Golgi network transport vesicle / clathrin-coated vesicle / Golgi cisterna membrane / Golgi Associated Vesicle Biogenesis / negative regulation of fat cell differentiation / endosome to lysosome transport / glucose import / neurotrophin TRK receptor signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / neuropeptide signaling pathway / clathrin-coated pit / ossification / response to insulin / endocytosis / cytoplasmic vesicle / regulation of gene expression / nuclear membrane / lysosome / early endosome / endosome membrane / G protein-coupled receptor signaling pathway / lysosomal membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Parthasarathy, G. / Soisson, S.M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2020 Title: Identification of potent inhibitors of the sortilin-progranulin interaction. Authors: Stachel, S.J. / Ginnetti, A.T. / Johnson, S.A. / Cramer, P. / Wang, Y. / Bukhtiyarova, M. / Krosky, D. / Stump, C. / Hurzy, D.M. / Schlegel, K.A. / Cooke, A.J. / Allen, S. / O'Donnell, G. / ...Authors: Stachel, S.J. / Ginnetti, A.T. / Johnson, S.A. / Cramer, P. / Wang, Y. / Bukhtiyarova, M. / Krosky, D. / Stump, C. / Hurzy, D.M. / Schlegel, K.A. / Cooke, A.J. / Allen, S. / O'Donnell, G. / Ziebell, M. / Parthasarathy, G. / Getty, K.L. / Ho, T. / Ou, Y. / Jovanovska, A. / Carroll, S.S. / Pausch, M. / Lumb, K. / Mosser, S.D. / Voleti, B. / Klein, D.J. / Soisson, S.M. / Zerbinatti, C. / Coleman, P.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6x48.cif.gz | 149.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6x48.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 6x48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/6x48 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/6x48 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6x3lC 6x4hC 3f6kS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74255.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SORT1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q99523 |
---|
-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 29 molecules
#4: Chemical | ChemComp-UP4 / |
---|---|
#5: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20-25% PEG3350, 0.4M Na Malonate, pH8, 0.1M Tris, 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.987 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Sep 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→64.63 Å / Num. obs: 24183 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.904→2.913 Å / Rmerge(I) obs: 0.592 / Num. unique obs: 252 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F6K Resolution: 2.9→64.63 Å / Cor.coef. Fo:Fc: 0.9271 / Cor.coef. Fo:Fc free: 0.8932 / SU R Cruickshank DPI: 0.754 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.655 / SU Rfree Blow DPI: 0.333 / SU Rfree Cruickshank DPI: 0.345
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.77 Å2 / Biso mean: 89.9 Å2 / Biso min: 36.77 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.438 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→64.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.03 Å / Total num. of bins used: 12
|