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- PDB-5sc4: CD44 PanDDA analysis group deposition -- The hyaluronan-binding d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5sc4 | ||||||
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Title | CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z927412236 | ||||||
![]() | CD44 antigen | ||||||
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Function / homology | ![]() Hyaluronan uptake and degradation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bradshaw, W.J. / Katis, V.L. / Bezerra, G.A. / Koekemoer, L. / von Delft, F. / Bountra, C. / Brennan, P.E. / Gileadi, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: CD44 PanDDA analysis group deposition Authors: Bradshaw, W.J. / Katis, V.L. / Bezerra, G.A. / Koekemoer, L. / von Delft, F. / Bountra, C. / Brennan, P.E. / Gileadi, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.2 KB | Display | ![]() |
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PDB format | ![]() | 67.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002221 (24 entries) |
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Title | CD44 PanDDA analysis group deposition |
Type | changed state |
Description | None |
-Related structure data
Related structure data | ![]() 2jcpS 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: 16970.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-8CN / ( | ||||||
#3: Chemical | ![]() #4: Chemical | ChemComp-EDO / | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % / Mosaicity: 0 ° |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200mM ammonium sulphate, 100mM MES, 24% PEG 5,000 MME |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.16→82.2 Å / Num. obs: 33905 / % possible obs: 69.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 7.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.028 / Rrim(I) all: 0.053 / Net I/σ(I): 34.2 / Num. measured all: 107189 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 2JCP Resolution: 1.165→20.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.047 / SU Rfree Blow DPI: 0.048 / SU Rfree Cruickshank DPI: 0.044
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Displacement parameters | Biso max: 118.02 Å2 / Biso mean: 12.29 Å2 / Biso min: 5.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.165→20.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.17→1.23 Å / Total num. of bins used: 51
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