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- PDB-6nda: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND CADMIUM -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nda | ||||||
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Title | RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND CADMIUM | ||||||
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![]() | CELL ADHESION/TOXIN / C-TYPE LECTIN / INTEGRIN / VENOM / COAGULATION / CELL ADHESION / CADMIUM / CELL ADHESION-TOXIN complex | ||||||
Function / homology | ![]() disruption of cell wall in another organism / collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / hypotonic response / response to L-ascorbic acid ...disruption of cell wall in another organism / collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / hypotonic response / response to L-ascorbic acid / oligosaccharide binding / skin morphogenesis / CHL1 interactions / Laminin interactions / basal part of cell / positive regulation of smooth muscle contraction / positive regulation of phagocytosis, engulfment / collagen-activated signaling pathway / peptidoglycan binding / Platelet Adhesion to exposed collagen / mammary gland development / hepatocyte differentiation / mesodermal cell differentiation / focal adhesion assembly / heparan sulfate proteoglycan binding / response to muscle activity / integrin complex / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / MET activates PTK2 signaling / cell adhesion mediated by integrin / Syndecan interactions / cell-substrate adhesion / positive regulation of epithelial cell migration / positive regulation of smooth muscle cell migration / response to amine / positive regulation of cell adhesion / ECM proteoglycans / positive regulation of collagen biosynthetic process / Integrin cell surface interactions / detection of mechanical stimulus involved in sensory perception of pain / axon terminus / laminin binding / collagen binding / cell-matrix adhesion / positive regulation of translation / cellular response to estradiol stimulus / integrin-mediated signaling pathway / female pregnancy / animal organ morphogenesis / positive regulation of smooth muscle cell proliferation / response to peptide hormone / cell-cell adhesion / cellular response to mechanical stimulus / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / integrin binding / virus receptor activity / signaling receptor activity / amyloid-beta binding / toxin activity / collagen-containing extracellular matrix / cell adhesion / response to hypoxia / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / positive regulation of cell population proliferation / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / extracellular space / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stetefeld, J. / McDougall, M.D. / Loewen, P.C. | ||||||
![]() | ![]() Title: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND CADMIUM Authors: Stetefeld, J. / McDougall, M.D. / Loewen, P.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 539.5 KB | Display | ![]() |
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PDB format | ![]() | 443.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 591.7 KB | Display | ![]() |
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Full document | ![]() | 647.2 KB | Display | |
Data in XML | ![]() | 94 KB | Display | |
Data in CIF | ![]() | 127.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5thpS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
-Snaclec rhodocetin subunit ... , 2 types, 12 molecules ADGJMPBEHKNQ
#1: Protein | Mass: 15741.510 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: D2YW39 #2: Protein | Mass: 14875.982 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: D2YW40 |
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-Protein , 1 types, 6 molecules CFILOR
#3: Protein | Mass: 23737.738 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 44 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CD / #6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-NH4 / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M TRIS, 2.65 M Ammonium SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 27, 2010 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.15→130.53 Å / Num. obs: 67910 / % possible obs: 94 % / Redundancy: 4.4 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.121 / Rsym value: 0.107 / Net I/av σ(I): 6.6 / Net I/σ(I): 10.9 / Num. measured all: 296700 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5THP Resolution: 3.15→92.47 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.848 / WRfactor Rfree: 0.2425 / WRfactor Rwork: 0.1966 / FOM work R set: 0.7914 / SU B: 22.861 / SU ML: 0.381 / SU Rfree: 0.5145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: MOLECULAR REPLACEMENT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.61 Å2 / Biso mean: 51.751 Å2 / Biso min: 3.87 Å2
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Refinement step | Cycle: final / Resolution: 3.15→92.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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