+Open data
-Basic information
Entry | Database: PDB / ID: 5dkq | ||||||||||||
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Title | Crystal Structure of Calcium-loaded S100B bound to SBi4214 | ||||||||||||
Components | Protein S100-B | ||||||||||||
Keywords | METAL BINDING PROTEIN/INHIBITOR / malignant melanoma / calcium binding / covalent inhibitor / METAL BINDING PROTEIN-INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information 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 / phosphorylation / axonogenesis / 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 / calcium ion binding / positive regulation of cell population proliferation / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 Å | ||||||||||||
Authors | Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Varney, K.M. ...Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Varney, K.M. / Toth, E.A. / MacKerell Jr., A.D. / Coop, A. / Weber, D.J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations. Authors: Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Charpentier, T.H. / Varney, K.M. / Toth, E.A. / ...Authors: Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Charpentier, T.H. / Varney, K.M. / Toth, E.A. / MacKerell, A.D. / Coop, A. / Weber, D.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dkq.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dkq.ent.gz | 23.3 KB | Display | PDB format |
PDBx/mmJSON format | 5dkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dkq_validation.pdf.gz | 663.9 KB | Display | wwPDB validaton report |
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Full document | 5dkq_full_validation.pdf.gz | 663.9 KB | Display | |
Data in XML | 5dkq_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 5dkq_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/5dkq ftp://data.pdbj.org/pub/pdb/validation_reports/dk/5dkq | HTTPS FTP |
-Related structure data
Related structure data | 5dknC 5dkrC 1mhoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10681.974 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: S100B / Production host: Escherichia coli (E. coli) / References: UniProt: P02638 | ||||
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#2: Chemical | #3: Chemical | ChemComp-5D0 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% Peg 3,350; 0.1M Bis-Tris, pH 7.5; 7.5mM CaCl2; 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127092 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.127092 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.59→38.43 Å / Num. obs: 13794 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 22.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Net I/σ(I): 23.3 / Num. measured all: 97324 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MHO Resolution: 1.591→38.427 Å / FOM work R set: 0.8163 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.53 / 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: 67.34 Å2 / Biso mean: 31.69 Å2 / Biso min: 17.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.591→38.427 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: 10
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