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Yorodumi- PDB-1psb: Solution structure of calcium loaded S100B complexed to a peptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1psb | ||||||
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Title | Solution structure of calcium loaded S100B complexed to a peptide from N-Terminal regulatory domain of NDR kinase. | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / HELIX-LOOP-HELIX / PROTEIN-PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information UFM1-modified protein reader activity / Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / postsynapse organization / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding ...UFM1-modified protein reader activity / Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / postsynapse organization / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production / mitogen-activated protein kinase kinase kinase binding / S100 protein binding / RHOBTB1 GTPase cycle / histone reader activity / RHOBTB2 GTPase cycle / negative regulation of MAP kinase activity / astrocyte activation / phosphorylation / axonogenesis / DNA damage checkpoint signaling / protein modification process / tau protein binding / calcium-dependent protein binding / regulation of translation / site of double-strand break / positive regulation of canonical NF-kappaB signal transduction / learning or memory / non-specific serine/threonine protein kinase / cell adhesion / intracellular signal transduction / cadherin binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA damage response / glutamatergic synapse / calcium ion binding / magnesium ion binding / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | SOLUTION NMR / Torsion Angle Dynamics, Restrained Molecular Dynamics, Simulated Annealing, | ||||||
Authors | Bhattacharya, S. / Large, E. / Heizmann, C.W. / Hemmings, B. / Chazin, W.J. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Structure of the Ca(2+)/S100B/NDR Kinase Peptide Complex: Insights into S100 Target Specificity and Activation of the Kinase. Authors: Bhattacharya, S. / Large, E. / Heizmann, C.W. / Hemmings, B. / Chazin, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1psb.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1psb.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 1psb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1psb_validation.pdf.gz | 372.7 KB | Display | wwPDB validaton report |
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Full document | 1psb_full_validation.pdf.gz | 716.8 KB | Display | |
Data in XML | 1psb_validation.xml.gz | 73.7 KB | Display | |
Data in CIF | 1psb_validation.cif.gz | 109.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/1psb ftp://data.pdbj.org/pub/pdb/validation_reports/ps/1psb | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10550.776 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: S100B / Plasmid: pH6 TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3) RIL / References: UniProt: P02638 #2: Protein/peptide | Mass: 3232.855 Da / Num. of mol.: 2 Fragment: N-terminal regulatory domain fragment, sequence database residue 60-85 Source method: obtained synthetically / Details: This sequence occurs naturally in Homo sapiens. / References: UniProt: Q15208 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Protein Backbone/Side-Chain Assignments were made from 3D CBCA(CO)NH, 3D HNCA, 3D HN(CO)CA, 3D HNCO 3D HCCH-TOCSY, 3D HCCH-COSY experiments. Peptide was assigned from 2D-Filtered COSY/TOCSY Experiments. |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Torsion Angle Dynamics, Restrained Molecular Dynamics, Simulated Annealing, Software ordinal: 1 Details: The structures are based on a total of 3274 restraints, 2964 are NOE-derived distance constraints and 310 dihedral angle restraints. | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 128 / Conformers submitted total number: 20 |