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- PDB-7l0e: Crystal structure of bovine RPE65 in complex with gem-difluoro em... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l0e | ||||||
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Title | Crystal structure of bovine RPE65 in complex with gem-difluoro emixustat and palmitate | ||||||
![]() | Retinoid isomerohydrolase | ||||||
![]() | HYDROLASE/INHIBITOR / non-heme iron / beta propeller / isomerohydrolase / isomerase / monotopic membrane protein / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() retinoid isomerohydrolase / lutein isomerase / retinol isomerase activity / all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity / all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity / zeaxanthin biosynthetic process / beta-carotene 15,15'-dioxygenase activity / The canonical retinoid cycle in rods (twilight vision) / retinal metabolic process / phosphatidylcholine binding ...retinoid isomerohydrolase / lutein isomerase / retinol isomerase activity / all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity / all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity / zeaxanthin biosynthetic process / beta-carotene 15,15'-dioxygenase activity / The canonical retinoid cycle in rods (twilight vision) / retinal metabolic process / phosphatidylcholine binding / cardiolipin binding / phosphatidylserine binding / visual perception / endoplasmic reticulum membrane / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kiser, P.D. | ||||||
![]() | ![]() Title: Rational Alteration of Pharmacokinetics of Chiral Fluorinated and Deuterated Derivatives of Emixustat for Retinal Therapy. Authors: Blum, E. / Zhang, J. / Zaluski, J. / Einstein, D.E. / Korshin, E.E. / Kubas, A. / Gruzman, A. / Tochtrop, G.P. / Kiser, P.D. / Palczewski, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.1 KB | Display | ![]() |
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PDB format | ![]() | 189 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7k88C ![]() 7k89C ![]() 7k8gC ![]() 4rscS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 3 - 533 / Label seq-ID: 3 - 533
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61040.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q28175, retinoid isomerohydrolase, lutein isomerase |
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-Non-polymers , 5 types, 851 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/XQ7.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/XQ7.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.99 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop Details: 30% PEG200, 100 mM Tris pH 8.5, 200 mM ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 118471 / % possible obs: 99.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.9→2.02 Å / Rmerge(I) obs: 2.482 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 19003 / CC1/2: 0.43 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RSC Resolution: 1.9→47.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.143 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127 Å2 / Biso mean: 44.77 Å2 / Biso min: 30.75 Å2
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Refinement step | Cycle: final / Resolution: 1.9→47.87 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 16930 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.904→1.953 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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