[English] 日本語
![](img/lk-miru.gif)
- PDB-6to7: Crystal structure of the Orexin-1 receptor in complex with suvore... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6to7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Orexin-1 receptor in complex with suvorexant at 2.29 A resolution | ||||||
![]() | Orexin receptor type 1 | ||||||
![]() | MEMBRANE PROTEIN / 7TM / GPCR | ||||||
Function / homology | ![]() orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / feeding behavior / peptide hormone binding / neuropeptide signaling pathway / cellular response to hormone stimulus / regulation of cytosolic calcium ion concentration / G protein-coupled receptor activity / peptide binding / G alpha (q) signalling events ...orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / feeding behavior / peptide hormone binding / neuropeptide signaling pathway / cellular response to hormone stimulus / regulation of cytosolic calcium ion concentration / G protein-coupled receptor activity / peptide binding / G alpha (q) signalling events / chemical synaptic transmission / positive regulation of ERK1 and ERK2 cascade / synapse / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rappas, M. / Ali, A. / Bennett, K.A. / Brown, J.D. / Bucknell, S.J. / Congreve, M. / Cooke, R.M. / Cseke, G. / de Graaf, C. / Dore, A.S. ...Rappas, M. / Ali, A. / Bennett, K.A. / Brown, J.D. / Bucknell, S.J. / Congreve, M. / Cooke, R.M. / Cseke, G. / de Graaf, C. / Dore, A.S. / Errey, J.C. / Jazayeri, A. / Marshall, F.H. / Mason, J.S. / Mould, R. / Patel, J.C. / Tehan, B.G. / Weir, M. / Christopher, J.A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-ray Crystallography and Computational Analysis. Authors: Rappas, M. / Ali, A.A.E. / Bennett, K.A. / Brown, J.D. / Bucknell, S.J. / Congreve, M. / Cooke, R.M. / Cseke, G. / de Graaf, C. / Dore, A.S. / Errey, J.C. / Jazayeri, A. / Marshall, F.H. / ...Authors: Rappas, M. / Ali, A.A.E. / Bennett, K.A. / Brown, J.D. / Bucknell, S.J. / Congreve, M. / Cooke, R.M. / Cseke, G. / de Graaf, C. / Dore, A.S. / Errey, J.C. / Jazayeri, A. / Marshall, F.H. / Mason, J.S. / Mould, R. / Patel, J.C. / Tehan, B.G. / Weir, M. / Christopher, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 281.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 227.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6todC ![]() 6tosC ![]() 6totC ![]() 6tp3C ![]() 6tp4C ![]() 6tp6C ![]() 6tpgC ![]() 6tpjC ![]() 6tpnC ![]() 6tq4C ![]() 6tq6C ![]() 6tq7C ![]() 6tq9C ![]() 4djhS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 45 molecules AB![](data/chem/img/SOG.gif)
![](data/chem/img/SOG.gif)
#1: Protein | Mass: 38132.852 Da / Num. of mol.: 2 Mutation: E46A I85L V95A R162L N194A L198A Y211A L304V C339A C375W C376W Source method: isolated from a genetically manipulated source Details: Suvorexant bound / Source: (gene. exp.) ![]() ![]() ![]() #5: Sugar | ChemComp-SOG / |
---|
-Non-polymers , 6 types, 159 molecules ![](data/chem/img/SUV.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/PGW.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/PGW.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PG4 / #4: Chemical | ChemComp-CIT / | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow | Temperature: 284 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.1M TRISODIUM CITRATE 50mM SODIUM CHLORIDE 50mM LITHIUM SULPHATE 15-34% PEG400 PH range: 3.0-6.5 / Temp details: Stable |
---|
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Stable / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 17, 2012 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→44.39 Å / Num. obs: 45066 / % possible obs: 92.9 % / Redundancy: 5.4 % / CC1/2: 0.985 / Rpim(I) all: 0.14 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.29→2.48 Å / Num. unique obs: 902 / CC1/2: 0.397 / % possible all: 52.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4DJH Resolution: 2.26→44.38 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.875 / SU R Cruickshank DPI: 0.258 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.247 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.203
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.25 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→44.38 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.26→2.48 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|