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Yorodumi- PDB-4np2: Crystal structure of the murine CD44 hyaluronan binding domain co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4np2 | ||||||
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Title | Crystal structure of the murine CD44 hyaluronan binding domain complex with a small molecule | ||||||
Components | CD44 antigen | ||||||
Keywords | Cell adhesion/inhibitor / Link module / Cell surface receptor / Hyaluronan / non-glycosylated / Cell surface / Cell adhesion-inhibitor complex | ||||||
Function / homology | Function and homology information Hyaluronan uptake and degradation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Cell surface interactions at the vascular wall / Integrin cell surface interactions / hyaluronan catabolic process ...Hyaluronan uptake and degradation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Cell surface interactions at the vascular wall / Integrin cell surface interactions / 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 / channel regulator activity / cargo receptor activity / wound healing, spreading of cells / cytokine receptor activity / 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 / 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 / Wnt signaling pathway / negative regulation of inflammatory response / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / neuron projection development / cell migration / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / membrane raft / apical plasma membrane / 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Liu, L.K. / Finzel, B. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4np2.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4np2.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 4np2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4np2_validation.pdf.gz | 463.7 KB | Display | wwPDB validaton report |
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Full document | 4np2_full_validation.pdf.gz | 464.1 KB | Display | |
Data in XML | 4np2_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 4np2_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/4np2 ftp://data.pdbj.org/pub/pdb/validation_reports/np/4np2 | HTTPS FTP |
-Related structure data
Related structure data | 4mrdC 4mreC 4mrfC 4mrgC 4mrhC 4np3C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Gene: Cd44, Cd44 Ly-24, Ly-24 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15379 |
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-Non-polymers , 5 types, 67 molecules
#2: Chemical | ChemComp-2L1 / | ||||
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#3: Chemical | ChemComp-MES / | ||||
#4: Chemical | #5: Chemical | ChemComp-DMS / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG MME 5000, MES, (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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2013 / Details: mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→40.08 Å / Num. all: 46025 / Num. obs: 14170 / % possible obs: 97.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 23.574 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.086 / Net I/σ(I): 11.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 31.75 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→40.08 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2134 / WRfactor Rwork: 0.1745 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8601 / SU B: 2.497 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1274 / SU Rfree: 0.1227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.123 / 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: 54.19 Å2 / Biso mean: 16.7488 Å2 / Biso min: 7.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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