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Open data
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Basic information
Entry | Database: PDB / ID: 4d5m | |||||||||
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Title | Gonadotropin-releasing hormone agonist | |||||||||
![]() | TRIPTORELIN | |||||||||
![]() | HORMONE / GNRH / LHRH / D-TRP / DECAPEPTIDE | |||||||||
Function / homology | ![]() negative regulation of immature T cell proliferation / neurosecretory vesicle / regulation of ovarian follicle development / response to corticosteroid / response to prolactin / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / Hormone ligand-binding receptors / : / response to prostaglandin E ...negative regulation of immature T cell proliferation / neurosecretory vesicle / regulation of ovarian follicle development / response to corticosteroid / response to prolactin / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / Hormone ligand-binding receptors / : / response to prostaglandin E / negative regulation of neuron migration / : / response to potassium ion / multicellular organism development / male sex determination / cytoplasmic side of rough endoplasmic reticulum membrane / Golgi-associated vesicle / response to testosterone / estrous cycle / axon terminus / female pregnancy / hormone activity / cell-cell signaling / regulation of gene expression / G alpha (q) signalling events / perikaryon / response to ethanol / response to lipopolysaccharide / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / dendrite / negative regulation of apoptotic process / signal transduction / mitochondrion / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | SYNTHETIC CONSTRUCT (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Legrand, P. / Le Du, M.-H. / Valery, C. / Deville-Foillard, S. / Paternostre, M. / Artzner, F. | |||||||||
![]() | ![]() Title: Atomic View of the Histidine Environment Stabilizing Higher- Ph Conformations of Ph-Dependent Proteins. Authors: Valery, C. / Deville-Foillard, S. / Lefebvre, C. / Taberner, N. / Legrand, P. / Meneau, F. / Meriadec, C. / Delvaux, C. / Bizien, T. / Kasotakis, E. / Lopez-Iglesias, C. / Gall, A. / ...Authors: Valery, C. / Deville-Foillard, S. / Lefebvre, C. / Taberner, N. / Legrand, P. / Meneau, F. / Meriadec, C. / Delvaux, C. / Bizien, T. / Kasotakis, E. / Lopez-Iglesias, C. / Gall, A. / Bressanelli, S. / Le Du, M.-H. / Paternostre, M. / Artzner, F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.1 KB | Display | ![]() |
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PDB format | ![]() | 39.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.2 KB | Display | ![]() |
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Full document | ![]() | 440.3 KB | Display | |
Data in XML | ![]() | 4.9 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein/peptide | Mass: 1312.458 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: TRIPTORELIN IS A MEDICINE AVAILABLE IN A NUMBER OF COUNTRIES WORLDWIDE. Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: UniProt: P01148*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | TRIPTORELI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.42 Å3/Da / Density % sol: 14 % / Description: NONE |
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Crystal grow | pH: 6.2 Details: 300 MM POTASSIUM PHOSPHATE BUFFER, PH 6.2 MIXED WITH 80 MG/ML TRIPTORELIN IN WATER. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2011 / Details: KB MIRRORS |
Radiation | Monochromator: CHANNEL-CUT MONOCHROMATOR SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.78471 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→41.95 Å / Num. obs: 24802 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 26.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 0.85→0.87 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.4 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: DIRECT METHODS Starting model: NONE Resolution: 0.85→41.95 Å / Cor.coef. Fo:Fc: 0.991 / Cor.coef. Fo:Fc free: 0.996 / SU B: 0.195 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 1.746 Å2
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Refinement step | Cycle: LAST / Resolution: 0.85→41.95 Å
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