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Yorodumi- PDB-5sbt: CD44 PanDDA analysis group deposition -- The hyaluronan-binding d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5sbt | ||||||
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Title | CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z445856640 | ||||||
Components | CD44 antigen | ||||||
Keywords | PROTEIN BINDING / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / antigen | ||||||
Function / homology | Function and homology information Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / negative regulation of regulatory T cell differentiation / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall ...Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / negative regulation of regulatory T cell differentiation / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process / wound healing involved in inflammatory response / monocyte aggregation / positive regulation of adaptive immune response / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of mature B cell apoptotic process / positive regulation of neutrophil apoptotic process / channel regulator activity / cellular response to fibroblast growth factor stimulus / cargo receptor activity / positive regulation of heterotypic cell-cell adhesion / 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 / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / Neutrophil degranulation / T cell activation / receptor-mediated endocytosis / cell projection / regulation of cell growth / phosphoprotein binding / Wnt signaling pathway / negative regulation of inflammatory response / cytokine-mediated signaling pathway / neuron projection development / cell migration / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / 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 / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / cell surface / protein-containing complex / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.16 Å | ||||||
Authors | Bradshaw, W.J. / Katis, V.L. / Bezerra, G.A. / Koekemoer, L. / von Delft, F. / Bountra, C. / Brennan, P.E. / Gileadi, O. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sbt.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sbt.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 5sbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/5sbt ftp://data.pdbj.org/pub/pdb/validation_reports/sb/5sbt | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Gene: Cd44, Ly-24 / Production host: Escherichia coli (E. coli) / References: UniProt: P15379 | ||||||
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#2: Chemical | ChemComp-VZP / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % / 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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91808 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91808 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.16→82.04 Å / Num. obs: 45587 / % possible obs: 93.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 9.45 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.074 / Rrim(I) all: 0.135 / Net I/σ(I): 8 / Num. measured all: 139369 / Scaling rejects: 812 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2JCP Resolution: 1.16→41.02 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.963 / SU R Cruickshank DPI: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.043 / SU Rfree Blow DPI: 0.045 / SU Rfree Cruickshank DPI: 0.042
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Displacement parameters | Biso max: 96.21 Å2 / Biso mean: 14.42 Å2 / Biso min: 6.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.16→41.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.16→1.17 Å / Total num. of bins used: 51
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