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- PDB-6hlo: Crystal structure of the Neurokinin 1 receptor in complex with th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hlo | ||||||
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Title | Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist Aprepitant | ||||||
![]() | Substance-P receptor,GlgA glycogen synthase,Substance-P receptor | ||||||
![]() | MEMBRANE PROTEIN / 7-TM / GPCR / Signalling protein | ||||||
Function / homology | ![]() substance P receptor activity / tachykinin receptor activity / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of flagellated sperm motility / positive regulation of uterine smooth muscle contraction / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / tachykinin receptor signaling pathway / positive regulation of lymphocyte proliferation ...substance P receptor activity / tachykinin receptor activity / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of flagellated sperm motility / positive regulation of uterine smooth muscle contraction / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / tachykinin receptor signaling pathway / positive regulation of lymphocyte proliferation / operant conditioning / sperm head / glycogen (starch) synthase activity / response to ozone / sperm ejaculation / positive regulation of action potential / response to auditory stimulus / smooth muscle contraction involved in micturition / regulation of smooth muscle cell proliferation / positive regulation of hormone secretion / positive regulation of blood pressure / positive regulation of vascular permeability / positive regulation of ossification / regulation of smooth muscle cell migration / glycogen biosynthetic process / positive regulation of leukocyte migration / eating behavior / positive regulation of epithelial cell migration / behavioral response to pain / associative learning / angiotensin-mediated drinking behavior / sperm flagellum / long-term memory / response to electrical stimulus / positive regulation of vasoconstriction / sperm midpiece / positive regulation of stress fiber assembly / positive regulation of epithelial cell proliferation / response to progesterone / positive regulation of synaptic transmission, GABAergic / response to nicotine / Cargo recognition for clathrin-mediated endocytosis / response to estradiol / Clathrin-mediated endocytosis / phospholipase C-activating G protein-coupled receptor signaling pathway / cell body / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / response to ethanol / inflammatory response / dendrite / cell surface / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schoppe, J. / Ehrenmann, J. / Klenk, C. / Rucktooa, P. / Schutz, M. / Dore, A.S. / Pluckthun, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists. Authors: Schoppe, J. / Ehrenmann, J. / Klenk, C. / Rucktooa, P. / Schutz, M. / Dore, A.S. / Pluckthun, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.9 KB | Display | ![]() |
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PDB format | ![]() | 182.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hllC ![]() 6hlpC ![]() 4zjcS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59148.160 Da / Num. of mol.: 1 Mutation: L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: TACR1, NK1R, TAC1R, PAB2292 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 96 molecules ![](data/chem/img/GBQ.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GBQ / | ||||
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#3: Chemical | ChemComp-CIT / | ||||
#4: Chemical | ChemComp-OLA / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.56 % / Description: Star-shaped |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 100 mM sodium citrate pH 6.0, 31% (v/v) PEG400, 50-70 mM MgCl2 and 50 uM aprepitant |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2017 / Details: Mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.24 Å / Num. obs: 32007 / % possible obs: 100 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 26.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3297 / CC1/2: 0.753 / Rpim(I) all: 0.571 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4ZJC Resolution: 2.4→29.442 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.442 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.0027 Å / Origin y: -11.0178 Å / Origin z: 58.478 Å
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Refinement TLS group | Selection details: all |