+Open data
-Basic information
Entry | Database: PDB / ID: 5ncg | ||||||
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Title | ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-9]-OH | ||||||
Components | Protein enabled homolog | ||||||
Keywords | CELL ADHESION / proline-rich motif / Ena/VASP inhibitor / actin / protein-protein interaction | ||||||
Function / homology | Function and homology information actin polymerization-dependent cell motility / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / lamellipodium ...actin polymerization-dependent cell motility / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / lamellipodium / cell junction / actin binding / cytoskeleton / focal adhesion / synapse / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å | ||||||
Authors | Barone, M. / Roske, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells. Authors: Barone, M. / Muller, M. / Chiha, S. / Ren, J. / Albat, D. / Soicke, A. / Dohmen, S. / Klein, M. / Bruns, J. / van Dinther, M. / Opitz, R. / Lindemann, P. / Beerbaum, M. / Motzny, K. / Roske, ...Authors: Barone, M. / Muller, M. / Chiha, S. / Ren, J. / Albat, D. / Soicke, A. / Dohmen, S. / Klein, M. / Bruns, J. / van Dinther, M. / Opitz, R. / Lindemann, P. / Beerbaum, M. / Motzny, K. / Roske, Y. / Schmieder, P. / Volkmer, R. / Nazare, M. / Heinemann, U. / Oschkinat, H. / Ten Dijke, P. / Schmalz, H.G. / Kuhne, R. #1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015 Title: A modular toolkit to inhibit proline-rich motif-mediated protein-protein interactions. Authors: Opitz, R. / Mueller, M. / Reuter, C. / Barone, M. / Soicke, A. / Roske, Y. / Piotukh, K. / Huy, P. / Beerbaum, M. / Wiesner, B. / Beyermann, M. / Schmieder, P. / Freund, C. / Volkmer, R. / ...Authors: Opitz, R. / Mueller, M. / Reuter, C. / Barone, M. / Soicke, A. / Roske, Y. / Piotukh, K. / Huy, P. / Beerbaum, M. / Wiesner, B. / Beyermann, M. / Schmieder, P. / Freund, C. / Volkmer, R. / Oschkinat, H. / Schmalz, H.G. / Kuehne, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ncg.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ncg.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ncg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ncg_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 5ncg_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 5ncg_validation.xml.gz | 19 KB | Display | |
Data in CIF | 5ncg_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/5ncg ftp://data.pdbj.org/pub/pdb/validation_reports/nc/5ncg | HTTPS FTP |
-Related structure data
Related structure data | 5n91C 5n9cSC 5n9pC 5najC 5nbfC 5nbxC 5nc2C 5nc7C 5ncfC 5ncpC 5nd0C 5nduC 5negC 6rcfC 6rcjC 6rd2C 6xvtC 6xxrC 7a5mC 7akiC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12628.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ENAH, MENA / Plasmid: pGEX-4T-1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8N8S7 #2: Chemical | ChemComp-8TB / ( #3: Chemical | ChemComp-NO3 / #4: 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: 1.88 Å3/Da / Density % sol: 34.7 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.2M ammonium sulfate, 200mM ammonium nitrate / Temp details: plate hotel |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→36.073 Å / Num. obs: 172743 / % possible obs: 91.4 % / Redundancy: 3 % / CC1/2: 0.999 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.02→1.08 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.49 / Num. unique obs: 26288 / CC1/2: 0.801 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N9C Resolution: 1.02→32.604 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 14.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→32.604 Å
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Refine LS restraints |
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LS refinement shell |
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