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- PDB-5otv: Extracellular domain of GLP-1 receptor in complex with GLP-1 vari... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5otv | ||||||
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Title | Extracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Cyc/Thr11Hcs | ||||||
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![]() | SIGNALING PROTEIN / glucagon-like peptide 1 / GPCR / cyclic peptides | ||||||
Function / homology | ![]() glucagon receptor binding / glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / negative regulation of execution phase of apoptosis / post-translational protein targeting to membrane, translocation / feeding behavior / response to psychosocial stress / regulation of heart contraction ...glucagon receptor binding / glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / negative regulation of execution phase of apoptosis / post-translational protein targeting to membrane, translocation / feeding behavior / response to psychosocial stress / regulation of heart contraction / positive regulation of calcium ion import / cellular response to glucagon stimulus / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / peptide hormone binding / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / protein kinase A signaling / activation of adenylate cyclase activity / negative regulation of blood pressure / cAMP-mediated signaling / positive regulation of peptidyl-threonine phosphorylation / response to activity / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / Glucagon signaling in metabolic regulation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / transmembrane signaling receptor activity / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / learning or memory / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mortensen, S. | ||||||
![]() | ![]() Title: alpha-Helix or beta-Turn? An Investigation into N-Terminally Constrained Analogues of Glucagon-like Peptide 1 (GLP-1) and Exendin-4. Authors: Oddo, A. / Mortensen, S. / Thogersen, H. / De Maria, L. / Hennen, S. / McGuire, J.N. / Kofoed, J. / Linderoth, L. / Reedtz-Runge, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.3 KB | Display | ![]() |
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PDB format | ![]() | 93.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.3 KB | Display | ![]() |
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Full document | ![]() | 445.4 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ottC ![]() 5otuC ![]() 5otwC ![]() 5otxC ![]() 4zgmS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13547.892 Da / Num. of mol.: 2 / Fragment: extracellular domain, UNP residues 24-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 3407.830 Da / Num. of mol.: 2 / Mutation: A8C, T11HCS / Source method: obtained synthetically / 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 Å3/Da / Density % sol: 38.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Morpheus from Molecular Dimensions, solution E5: 0.12 M Ethylene Glycols, 0.1 M Buffer System 2 pH 7.5, 205 (v/v) PEg500mme, 10% (w/v) PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Feb 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.62 Å / Num. obs: 17691 / % possible obs: 98 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.092 / Rsym value: 0.204 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 7.04 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 5.8 / Num. measured obs: 8233 / Num. unique all: 1170 / CC1/2: 0.962 / Rpim(I) all: 0.158 / Rrim(I) all: 0.428 / % possible all: 91.98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZGM Resolution: 2→42.616 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→42.616 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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