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Yorodumi- PDB-6ndb: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND COBALT -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ndb | ||||||
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Title | RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND COBALT | ||||||
Components |
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Keywords | CELL ADHESION/TOXIN / C-TYPE LECTIN / INTEGRIN / VENOM / COAGULATION / CELL ADHESION / CELL ADHESION-TOXIN complex | ||||||
Function / homology | Function and homology information 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 / CHL1 interactions / Laminin interactions / skin morphogenesis / basal part of cell / positive regulation of smooth muscle contraction / positive regulation of phagocytosis, engulfment / collagen-activated signaling pathway / peptidoglycan binding / mammary gland development / Platelet Adhesion to exposed collagen / hepatocyte differentiation / mesodermal cell differentiation / focal adhesion assembly / heparan sulfate proteoglycan binding / integrin complex / response to muscle activity / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / cell adhesion mediated by integrin / MET activates PTK2 signaling / 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 / cellular response to estradiol stimulus / positive regulation of smooth muscle cell proliferation / extracellular matrix organization / cell-matrix adhesion / integrin-mediated signaling pathway / positive regulation of translation / female pregnancy / animal organ morphogenesis / cell-cell adhesion / cellular response to mechanical stimulus / response to peptide hormone / integrin binding / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / virus receptor activity / signaling receptor activity / amyloid-beta binding / collagen-containing extracellular matrix / toxin activity / response to hypoxia / cell adhesion / 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 | Homo sapiens (human) Calloselasma rhodostoma (Malayan pit viper) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 3.2 Å | ||||||
Authors | Stetefeld, J. / McDougall, M.D. / Loewen, P.C. | ||||||
Citation | Journal: To be published Title: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND COBALT Authors: Stetefeld, J. / McDougall, M.D. / Loewen, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ndb.cif.gz | 540.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ndb.ent.gz | 443.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ndb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/6ndb ftp://data.pdbj.org/pub/pdb/validation_reports/nd/6ndb | HTTPS FTP |
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-Related structure data
Related structure data | 5thpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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) Calloselasma rhodostoma (Malayan pit viper) References: UniProt: D2YW39 #2: Protein | Mass: 14875.982 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Calloselasma rhodostoma (Malayan pit viper) 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.) Homo sapiens (human) / Gene: ITGA2, CD49B / Production host: Escherichia coli (E. coli) / References: UniProt: P17301 |
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-Non-polymers , 6 types, 44 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CO / #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 27, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→131.836 Å / Num. obs: 70033 / % possible obs: 99.2 % / Redundancy: 6.2 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.148 / Rsym value: 0.136 / Net I/av σ(I): 5.2 / Net I/σ(I): 11.6 / Num. measured all: 436426 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5THP Resolution: 3.2→47.07 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.825 / SU B: 24.239 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.545 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 208.33 Å2 / Biso mean: 62.929 Å2 / Biso min: 21.14 Å2
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Refinement step | Cycle: final / Resolution: 3.2→47.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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