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- PDB-4jvf: The Crystal structure of PDE6D in complex with the inhibitor (s)-5 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jvf | ||||||
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Title | The Crystal structure of PDE6D in complex with the inhibitor (s)-5 | ||||||
![]() | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | ||||||
![]() | Protein binding/inhibitor / Immunoglobulin-like beta-sandwich / GDI-like solubilizing factor / Prenyl binding / Protein binding-inhibitor complex | ||||||
Function / homology | ![]() ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / small GTPase binding / cilium / RAS processing / cytoplasmic vesicle / cytoskeleton ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / small GTPase binding / cilium / RAS processing / cytoplasmic vesicle / cytoskeleton / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gunther, Z. / Papke, B. / Ismail, S. / Vartak, N. / Chandra, A. / Hoffmann, M. / Hahn, S. / Triola, G. / Wittinghofer, A. / Bastiaens, P. / Waldmann, H. | ||||||
![]() | ![]() Title: Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling Authors: Zimmermann, G. / Papke, B. / Ismail, S. / Vartak, N. / Chandra, A. / Hoffmann, M. / Hahn, S.A. / Triola, G. / Wittinghofer, A. / Bastiaens, P.I. / Waldmann, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46 KB | Display | ![]() |
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PDB format | ![]() | 31.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 773.1 KB | Display | ![]() |
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Full document | ![]() | 775.4 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jv6C ![]() 4jv8C ![]() 4jvbC ![]() 3t5gS C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 17585.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-17X / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 18% PEG 4000, 25mM Sodium Acetate, 200mM Ammonium Sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2012 |
Radiation | Monochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→27.9 Å / Num. all: 8659 / Num. obs: 8659 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.122 |
Reflection shell | Resolution: 2.4→2.5 Å / % possible all: 98.8 |
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Processing
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Refinement | Starting model: 3T5G Resolution: 2.4→27.9 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.48 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.317 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 31.222 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→27.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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