[English] 日本語
Yorodumi- PDB-5x74: The crystal Structure PDE delta in complex with compound (R, R)-1g -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x74 | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal Structure PDE delta in complex with compound (R, R)-1g | ||||||
Components | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | ||||||
Keywords | LIPID BINDING PROTEIN | ||||||
Function / homology | Function and homology information ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Jiang, Y. / Zhuang, C. / Chen, L. / Wang, R. / Wang, F. / Sheng, C. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Structural Biology-Inspired Discovery of Novel KRAS-PDE delta Inhibitors Authors: Jiang, Y. / Zhuang, C. / Chen, L. / Lu, J. / Dong, G. / Miao, Z. / Zhang, W. / Li, J. / Sheng, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5x74.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5x74.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 5x74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x74_validation.pdf.gz | 767.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5x74_full_validation.pdf.gz | 769.5 KB | Display | |
Data in XML | 5x74_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 5x74_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/5x74 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/5x74 | HTTPS FTP |
-Related structure data
Related structure data | 5x72C 5x73C 4jv6S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17398.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli (E. coli) / References: UniProt: O43924 |
---|---|
#2: Chemical | ChemComp-JAY / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.41 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Sodium acetate, 30 %(v/v) PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97913 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: AREA DETECTOR / Date: Oct 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97913 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 10393 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.04 / Χ2: 1.041 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 11.93 / Num. unique obs: 498 / Rpim(I) all: 0.208 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JV6 Resolution: 2.25→36.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.736 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.043 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.307 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.25→36.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|