+Open data
-Basic information
Entry | Database: PDB / ID: 6i18 | ||||||
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Title | CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH BDP-13176 | ||||||
Components | Fascin | ||||||
Keywords | STRUCTURAL PROTEIN / actin bundling / small molecule inhibition | ||||||
Function / homology | Function and homology information microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / podosome / positive regulation of podosome assembly / cell-cell junction assembly ...microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / podosome / positive regulation of podosome assembly / cell-cell junction assembly / positive regulation of filopodium assembly / establishment or maintenance of cell polarity / actin filament bundle assembly / microvillus / positive regulation of lamellipodium assembly / stress fiber / ruffle / filopodium / cell motility / regulation of actin cytoskeleton organization / cell-cell junction / actin filament binding / actin cytoskeleton / cell migration / lamellipodium / protein-macromolecule adaptor activity / actin binding / cell cortex / actin cytoskeleton organization / growth cone / Interleukin-4 and Interleukin-13 signaling / cytoskeleton / cadherin binding / RNA binding / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Schuettelkopf, A.W. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2019 Title: Structure-based design, synthesis and biological evaluation of a novel series of isoquinolone and pyrazolo[4,3-c]pyridine inhibitors of fascin 1 as potential anti-metastatic agents. Authors: Francis, S. / Croft, D. / Schuttelkopf, A.W. / Parry, C. / Pugliese, A. / Cameron, K. / Claydon, S. / Drysdale, M. / Gardner, C. / Gohlke, A. / Goodwin, G. / Gray, C.H. / Konczal, J. / ...Authors: Francis, S. / Croft, D. / Schuttelkopf, A.W. / Parry, C. / Pugliese, A. / Cameron, K. / Claydon, S. / Drysdale, M. / Gardner, C. / Gohlke, A. / Goodwin, G. / Gray, C.H. / Konczal, J. / McDonald, L. / Mezna, M. / Pannifer, A. / Paul, N.R. / Machesky, L. / McKinnon, H. / Bower, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i18.cif.gz | 221.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i18.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 6i18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i18_validation.pdf.gz | 802.6 KB | Display | wwPDB validaton report |
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Full document | 6i18_full_validation.pdf.gz | 804.4 KB | Display | |
Data in XML | 6i18_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 6i18_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/6i18 ftp://data.pdbj.org/pub/pdb/validation_reports/i1/6i18 | HTTPS FTP |
-Related structure data
Related structure data | 6i0zC 6i10SC 6i11C 6i12C 6i13C 6i14C 6i15C 6i16C 6i17C S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 54601.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FSCN1, FAN1, HSN, SNL / Plasmid: pBDDP-SPR3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q16658 | ||||
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#2: Chemical | ChemComp-ACT / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-H0N / | #5: 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: 2.36 Å3/Da / Density % sol: 47.82 % / Mosaicity: 0.214 ° |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 18-22% PEG 8000, 100-130 mM MgAc2, 100 mM citric acid pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→49.35 Å / Num. obs: 84863 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.368 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 18 / Num. measured all: 543840 |
Reflection shell | Resolution: 1.49→1.53 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.014 / Mean I/σ(I) obs: 1.7 / Rpim(I) all: 0.464 / Rrim(I) all: 1.195 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I10 Resolution: 1.49→49.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.176 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.068 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 64.29 Å2 / Biso mean: 26.229 Å2 / Biso min: 13.28 Å2
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Refinement step | Cycle: final / Resolution: 1.49→49.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.49→1.529 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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