+Open data
-Basic information
Entry | Database: PDB / ID: 5ndu | ||||||
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Title | ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-12]-OMe | ||||||
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: 1.42 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 | 5ndu.cif.gz | 157 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ndu.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ndu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ndu_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5ndu_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5ndu_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 5ndu_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5ndu ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5ndu | HTTPS FTP |
-Related structure data
Related structure data | 5n91C 5n9cC 5n9pC 5najC 5nbfC 5nbxC 5nc2C 5nc7C 5ncfC 5ncgSC 5ncpC 5nd0C 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
-Protein , 1 types, 2 molecules AB
#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: Q8N8S7 |
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-Non-polymers , 5 types, 168 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Chemical | #6: 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: 2.03 Å3/Da / Density % sol: 39.5 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0M ammonium sulfate, 220mM 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: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→43.9378 Å / Num. obs: 38981 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rrim(I) all: 0.12 / Net I/σ(I): 11.36 |
Reflection shell | Resolution: 1.42→1.5 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.25 / Num. unique obs: 5881 / CC1/2: 0.593 / Rrim(I) all: 1.714 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NCG Resolution: 1.42→43.917 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.59 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→43.917 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | T23: -0.0035 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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