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- PDB-5d65: X-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d65 | |||||||||
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Title | X-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3) WITH HEPARIN COMPLEX | |||||||||
![]() | C-C motif chemokine 3 | |||||||||
![]() | CYTOKINE / CC chemokine / CCL3 / OLIGOMER / SIGNALING PROTEIN / HEPARIN / GAG / COMPLEX | |||||||||
Function / homology | ![]() granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation ...granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain / negative regulation of bone mineralization / CCR chemokine receptor binding / positive regulation of microglial cell activation / cell activation / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / phospholipase activator activity / macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / exocytosis / negative regulation of osteoclast differentiation / monocyte chemotaxis / Interleukin-10 signaling / cellular response to interleukin-1 / negative regulation by host of viral transcription / cytoskeleton organization / positive regulation of calcium-mediated signaling / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / calcium-mediated signaling / response to toxic substance / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of inflammatory response / osteoblast differentiation / chemotaxis / calcium ion transport / positive regulation of neuron apoptotic process / MAPK cascade / positive regulation of tumor necrosis factor production / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / cellular response to tumor necrosis factor / kinase activity / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / inflammatory response / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liang, W.G. / Hwang, D.Y. / Zulueta, M.M. / Hung, S.C. / Tang, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3. Authors: Liang, W.G. / Triandafillou, C.G. / Huang, T.Y. / Zulueta, M.M. / Banerjee, S. / Dinner, A.R. / Hung, S.C. / Tang, W.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.6 KB | Display | ![]() |
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PDB format | ![]() | 124.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5cmdC ![]() 5corC ![]() 5coyC ![]() 5dnfC ![]() 2x69S 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
#1: Protein | Mass: 7793.664 Da / Num. of mol.: 5 / Fragment: UNP residues 23-92 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-BGC / #4: Chemical | #5: Sugar | ChemComp-GLC / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.82 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Tris, pH 7.0; 1.8M (NH4)2SO4; / PH range: 7.0-7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 11, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.746 Å / Relative weight: 1 |
Reflection | Resolution: 3.095→34.22 Å / Num. obs: 14085 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 12.9 % / Rmerge(I) obs: 0.053 / Rsym value: 0.039 / Net I/σ(I): 48.9 |
Reflection shell | Resolution: 3.1→3.13 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2X69 Resolution: 3.1→34.22 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.18 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→34.22 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 22.7769 Å / Origin y: 73.9483 Å / Origin z: 46.6755 Å
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Refinement TLS group | Selection details: ALL |