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- PDB-4mrf: Crystal structure of the murine cd44 hyaluronan binding domain co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mrf | ||||||
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Title | Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule | ||||||
![]() | CD44 antigen | ||||||
![]() | Cell adhesion/inhibitor / Link module / Cell receptor / Hyaluronan binding / Cell surface / Cell adhesion-inhibitor complex | ||||||
Function / homology | ![]() Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process ...Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process / wound healing involved in inflammatory response / positive regulation of adaptive immune response / positive regulation of neutrophil apoptotic process / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / negative regulation of CD4-positive, alpha-beta T cell proliferation / cargo receptor activity / wound healing, spreading of cells / branching involved in ureteric bud morphogenesis / epidermal growth factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / channel regulator activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / regulation of cell growth / phosphoprotein binding / negative regulation of inflammatory response / transmembrane signaling receptor activity / Wnt signaling pathway / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / neuron projection development / cell migration / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / inflammatory response / membrane raft / external side of plasma membrane / positive regulation of gene expression / protein kinase binding / cell surface / protein-containing complex / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Liu, L.K. / Finzel, B. | ||||||
![]() | ![]() Title: Fragment-Based Identification of an Inducible Binding Site on Cell Surface Receptor CD44 for the Design of Protein-Carbohydrate Interaction Inhibitors. Authors: Liu, L.K. / Finzel, B.C. #1: ![]() Title: Structures of the Cd44-hyaluronan complex provide insight into a fundamental carbohydrate-protein interaction. Authors: Banerji, S. / Wright, A.J. / Noble, M. / Mahoney, D.J. / Campbell, I.D. / Day, A.J. / Jackson, D.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.1 KB | Display | ![]() |
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PDB format | ![]() | 32.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468 KB | Display | ![]() |
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Full document | ![]() | 468.9 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mrdC ![]() 4mreC ![]() 4mrgC ![]() 4mrhC ![]() 4np2C ![]() 4np3C ![]() 2jcpS 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, 1 molecules A
#1: Protein | Mass: 16724.604 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 23-171 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 64 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/2CK.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/2CK.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DMS / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-2CK / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG MME 5000, 100 mM MES, 200 mM (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→40.8 Å / Num. all: 20312 / Num. obs: 20192 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.042 / Net I/σ(I): 22.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 32.19 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2JCP Resolution: 1.55→40.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2215 / WRfactor Rwork: 0.1864 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8846 / SU B: 1.385 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0886 / SU Rfree: 0.0898 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 46.71 Å2 / Biso mean: 13.8573 Å2 / Biso min: 2.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→40.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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