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Open data
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Basic information
Entry | Database: PDB / ID: 4pdz | ||||||||||||
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Title | Crystal Structure of Calcium-loaded S100B bound to SBi4172 | ||||||||||||
![]() | Protein S100-B | ||||||||||||
![]() | METAL BINDING PROTEIN/INHIBITOR / Malignant Melanoma / Calcium Binding / Covalent Inhibitor / Complex / METAL BINDING PROTEIN-INHIBITOR complex | ||||||||||||
Function / homology | ![]() Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / 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 / S100 protein binding ...Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / 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 / S100 protein binding / axonogenesis / sarcoplasmic reticulum / astrocyte activation / tau protein binding / calcium-dependent protein binding / regulation of translation / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / phosphorylation / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Cavalier, M.C. / Pierce, A.D. / Wilder, P.T. / Neau, D. / Toth, E.A. / Weber, D.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Covalent Small Molecule Inhibitors of Ca(2+)-Bound S100B. Authors: Cavalier, M.C. / Pierce, A.D. / Wilder, P.T. / Alasady, M.J. / Hartman, K.G. / Neau, D.B. / Foley, T.L. / Jadhav, A. / Maloney, D.J. / Simeonov, A. / Toth, E.A. / Weber, D.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 | ![]() | 55 KB | Display | ![]() |
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PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 717.8 KB | Display | ![]() |
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Full document | ![]() | 719 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pe0C ![]() 4pe1C ![]() 4pe4C ![]() 4pe7C ![]() 1mhoS 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: 10681.974 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CTI / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% 2-methyl-2,4-pentanediol, 0.1M Hepes, 7.5mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→35.26 Å / Num. all: 17118 / Num. obs: 17118 / % possible obs: 92.6 % / Redundancy: 3.2 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.046 / Rsym value: 0.038 / Net I/av σ(I): 8.188 / Net I/σ(I): 13.8 / Num. measured all: 55396 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MHO Resolution: 1.73→35.26 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.72 Å2 / Biso mean: 39.0003 Å2 / Biso min: 23.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.73→35.26 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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