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- PDB-4k72: CFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36-V... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4k72 | ||||||
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Title | CFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36-VQD (ANSRVQDSII) | ||||||
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![]() | PEPTIDE BINDING PROTEIN/PROTEIN BINDING / PDZ domain / CAL / PIST / FIG / PDZ-peptide complex / CFTR Associated Ligand / CFTR / PEPTIDE BINDING PROTEIN-PROTEIN BINDING complex | ||||||
Function / homology | ![]() negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / trans-Golgi network transport vesicle / molecular sequestering activity / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport ...negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / trans-Golgi network transport vesicle / molecular sequestering activity / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / transmembrane transporter binding / postsynaptic density / Golgi membrane / lysosomal membrane / dendrite / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Amacher, J.F. / Madden, D.R. | ||||||
![]() | ![]() Title: Stereochemical Preferences Modulate Affinity and Selectivity among Five PDZ Domains that Bind CFTR: Comparative Structural and Sequence Analyses. Authors: Amacher, J.F. / Cushing, P.R. / Brooks, L. / Boisguerin, P. / Madden, D.R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.9 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4joeC ![]() 4jofC ![]() 4jogC ![]() 4johC ![]() 4jojC ![]() 4jokC ![]() 4jopC ![]() 4jorC ![]() 4k6yC ![]() 4k75C ![]() 4k76C ![]() 4k78C ![]() 4e34S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9353.722 Da / Num. of mol.: 2 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1103.208 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 40% (w/v) polyethylene glycol (PEG) 1000, 0.1 M sodium thiosulfate pentahydrate, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 27, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→19.57 Å / Num. all: 15231 / Num. obs: 15168 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.59 / Rmerge(I) obs: 0.128 / Rsym value: 0.065 / Net I/σ(I): 15.58 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4E34 (CAL PDZ domain bound to iCAL36 peptide) Resolution: 1.9→19.57 Å / SU ML: 0.28 / Cross valid method: Omit map / σ(F): 2 / σ(I): 3.59 / Phase error: 22.09 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.589 Å2 / ksol: 0.417 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.57 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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