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Yorodumi- PDB-7k89: Crystal structure of bovine RPE65 in complex with 4-fluoro-emixus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k89 | ||||||
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Title | Crystal structure of bovine RPE65 in complex with 4-fluoro-emixustat and palmitate | ||||||
Components | Retinoid isomerohydrolase | ||||||
Keywords | ISOMERASE / HYDROLASE/INHIBITOR / Non-heme iron / isomerohydrolase / inhibitor / beta-propeller / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / cardiolipin 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 / cardiolipin binding / phosphatidylcholine binding / response to stimulus / phosphatidylserine binding / visual perception / endoplasmic reticulum membrane / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Kiser, P.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k89.cif.gz | 240.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k89.ent.gz | 189 KB | Display | PDB format |
PDBx/mmJSON format | 7k89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k89_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7k89_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 7k89_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 7k89_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/7k89 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/7k89 | HTTPS FTP |
-Related structure data
Related structure data | 7k88C 7k8gC 7l0eC 4rseS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: 2 - 533 / Label seq-ID: 2 - 533
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60935.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: Q28175, retinoid isomerohydrolase, lutein isomerase |
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-Non-polymers , 6 types, 810 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.98 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: Same as for entry 4RSE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 82432 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.15→2.28 Å / Rmerge(I) obs: 1.77 / Num. unique obs: 13267 / CC1/2: 0.408 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4RSE Resolution: 2.15→47.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.725 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.694 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→47.84 Å
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