+Open data
-Basic information
Entry | Database: PDB / ID: 5ml6 | |||||||||
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Title | The crystal structure of PDE6D in complex to inhibitor-8 | |||||||||
Components | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | |||||||||
Keywords | LIPID BINDING PROTEIN / Prenyl binding protein / farnesylated KRas / Plasma membrane / Arl2 | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | |||||||||
Authors | Fansa, E.K. / Martin-gago, P. / Waldmann, H. / Wittinghofer, A. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: A PDE6 delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2. Authors: Martin-Gago, P. / Fansa, E.K. / Klein, C.H. / Murarka, S. / Janning, P. / Schurmann, M. / Metz, M. / Ismail, S. / Schultz-Fademrecht, C. / Baumann, M. / Bastiaens, P.I. / Wittinghofer, A. / Waldmann, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ml6.cif.gz | 48.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ml6.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ml6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ml6_validation.pdf.gz | 722.7 KB | Display | wwPDB validaton report |
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Full document | 5ml6_full_validation.pdf.gz | 725.8 KB | Display | |
Data in XML | 5ml6_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 5ml6_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/5ml6 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/5ml6 | HTTPS FTP |
-Related structure data
Related structure data | 5ml2C 5ml3C 5ml4C 5ml8C 3t5gS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17309.793 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 |
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#2: Chemical | ChemComp-9GD / |
#3: 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: 3.05 Å3/Da / Density % sol: 59.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M NaOAc, pH 4.6, 30 % PEG 4000, 0.2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→27.88 Å / Num. obs: 16799 / % possible obs: 99.6 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.2 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T5G Resolution: 1.87→27.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.259 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.129 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.94 Å2 / Biso mean: 26.384 Å2 / Biso min: 12.78 Å2
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Refinement step | Cycle: final / Resolution: 1.87→27.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.918 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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