+Open data
-Basic information
Entry | Database: PDB / ID: 5x72 | ||||||
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Title | The crystal Structure PDE delta in complex with (rac)-p9 | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Jiang, Y. / Zhuang, C. / Chen, L. / Wang, R. / Wang, F. / Sheng, C. | ||||||
Funding support | China, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x72.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x72.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 5x72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x72_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5x72_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5x72_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 5x72_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/5x72 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/5x72 | HTTPS FTP |
-Related structure data
Related structure data | 5x73C 5x74C 4jv6S C: citing same article (ref.) S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17440.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43924 |
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#2: Chemical | ChemComp-P59 / ( |
#3: Chemical | ChemComp-P69 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium citrate dibasic, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: AREA DETECTOR / Date: Dec 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 15663 / % possible obs: 99.7 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Χ2: 0.975 / Net I/σ(I): 38.61 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 7.4 / Num. unique obs: 774 / Rpim(I) all: 0.132 / Χ2: 0.935 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JV6 Resolution: 1.95→48.12 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.541 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.645 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→48.12 Å
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Refine LS restraints |
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