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Open data
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Basic information
Entry | Database: PDB / ID: 4zmv | ||||||
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Title | Crystal structure of human P-cadherin (ss-X-dimer pocket I) | ||||||
![]() | Cadherin-3 | ||||||
![]() | CELL ADHESION / dimerization / conformational change | ||||||
Function / homology | ![]() negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Adherens junctions interactions / catenin complex ...negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Adherens junctions interactions / catenin complex / retina homeostasis / cell-cell junction assembly / adherens junction organization / positive regulation of insulin-like growth factor receptor signaling pathway / keratinization / homophilic cell adhesion via plasma membrane adhesion molecules / visual perception / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / cell morphogenesis / positive regulation of canonical Wnt signaling pathway / cell junction / cell adhesion / response to xenobiotic stimulus / cadherin binding / calcium ion binding / positive regulation of gene expression / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caaveiro, J.M.M. / Kudo, S. / Tsumoto, K. | ||||||
![]() | ![]() Title: Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism Authors: Kudo, S. / Caaveiro, J.M. / Tsumoto, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.5 KB | Display | ![]() |
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PDB format | ![]() | 145.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
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Full document | ![]() | 459.3 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zmlC ![]() 4zmnSC ![]() 4zmoC ![]() 4zmpC ![]() 4zmqC ![]() 4zmtC ![]() 4zmwC ![]() 4zmxC ![]() 4zmyC ![]() 4zmzC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23447.102 Da / Num. of mol.: 2 / Fragment: UNP residues 108-320 / Mutation: V4I, A5P, N22V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 92 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.55 Å3/Da / Density % sol: 72.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.2 M Lithium sulfate 10 mM nickel sulfate 100 mM TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.1 Å / Num. obs: 33412 / % possible obs: 98.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.6 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZMN Resolution: 2.4→45.1 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.673 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.191 / 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: 49.076 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→45.1 Å
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Refine LS restraints |
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