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- PDB-8d52: Parathyroid hormone 1 receptor extracellular domain complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d52 | |||||||||
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Title | Parathyroid hormone 1 receptor extracellular domain complexed with a peptide ligand containing (2-naphthyl)-beta-3-homoalanine | |||||||||
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![]() | SIGNALING PROTEIN / parathyroid hormone 1 receptor / signaling / beta-amino acid | |||||||||
Function / homology | ![]() negative regulation of chondrocyte development / regulation of chondrocyte differentiation / parathyroid hormone receptor activity / cAMP metabolic process / G protein-coupled peptide receptor activity / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / peptide hormone receptor binding / positive regulation of inositol phosphate biosynthetic process ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / parathyroid hormone receptor activity / cAMP metabolic process / G protein-coupled peptide receptor activity / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / peptide hormone receptor binding / positive regulation of inositol phosphate biosynthetic process / bone mineralization / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / epidermis development / chondrocyte differentiation / cell maturation / bone resorption / skeletal system development / female pregnancy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / intracellular calcium ion homeostasis / : / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / regulation of gene expression / basolateral plasma membrane / in utero embryonic development / cell population proliferation / cell surface receptor signaling pathway / receptor complex / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yu, Z. / Kreitler, D.F. / Gellman, S.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification. Authors: Yu, Z. / Kreitler, D.F. / Chiu, Y.T.T. / Xu, R. / Bruchs, A.T. / Bingman, C.A. / Gellman, S.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.9 KB | Display | ![]() |
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PDB format | ![]() | 49.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.8 KB | Display | ![]() |
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Full document | ![]() | 451.1 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d51C ![]() 3h3gS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11995.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2833.294 Da / Num. of mol.: 1 Mutation: I31 substituted by (2-naphthyl)-beta-3-homoalanine Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) ![]() |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 28 % v/v PEG Smear Low, 0.1 M tris-HCl pH 8, 0.15 M Sodium citrate, 1% ethylene glycol, 1 mM ZnSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2022 / Details: KB |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920105 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→68.403 Å / Num. obs: 7246 / % possible obs: 81.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 42.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.088 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.02→2.163 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.123 / Num. unique obs: 361 / CC1/2: 0.551 / Rpim(I) all: 0.791 / % possible all: 22.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3h3g Resolution: 2.02→48.3 Å / SU ML: 0.2504 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.8938 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: 53.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→48.3 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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