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- PDB-6v2d: Crystal Structure of chromodomain of CDYL2 in complex with inhibi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6v2d | ||||||
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Title | Crystal Structure of chromodomain of CDYL2 in complex with inhibitor UNC3866 | ||||||
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![]() | GENE REGULATION / structural genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() methylated histone binding / transcription corepressor activity / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Authors: Dong, C. / Liu, Y. / Lyu, T.J. / Beldar, S. / Lamb, K.N. / Tempel, W. / Li, Y. / Li, Z. / James, L.I. / Qin, S. / Wang, Y. / Min, J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.6 KB | Display | ![]() |
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PDB format | ![]() | 77.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.9 KB | Display | ![]() |
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Full document | ![]() | 490.2 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2mj8C ![]() 6v2hC ![]() 6v2rC ![]() 6v2sC ![]() 6v3nC ![]() 6v41C ![]() 6v8wC ![]() 5epjS ![]() 5epkS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7695.596 Da / Num. of mol.: 6 / Fragment: Chromodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% P3350, 0.2M ammonium acetate, 0.1M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 23, 2014 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→38.43 Å / Num. obs: 28615 / % possible obs: 92.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.116 / Net I/σ(I): 14.7 | ||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: preliminary coordinates of PDB entries 5EPJ and 5EPK Resolution: 2.1→38.05 Å / SU ML: 0.259 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 27.1204 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→38.05 Å
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Refine LS restraints |
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LS refinement shell |
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