+Open data
-Basic information
Entry | Database: PDB / ID: 6tu9 | ||||||
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Title | The ROR1 Pseudokinase Domain Bound To Ponatinib | ||||||
Components | Inactive tyrosine-protein kinase transmembrane receptor ROR1 | ||||||
Keywords | SIGNALING PROTEIN / Receptor Transmembrane Kinase Pseudokinase Small-molecule inhibitor | ||||||
Function / homology | Function and homology information WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / axon terminus / stress fiber / transmembrane receptor protein tyrosine kinase activity / sensory perception of sound ...WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / axon terminus / stress fiber / transmembrane receptor protein tyrosine kinase activity / sensory perception of sound / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of neuron projection development / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / receptor complex / phosphorylation / cell surface / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Mathea, S. / Preuss, F. / Chatterjee, D. / Niininen, W. / Ungureanu, D. / Shin, D. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2020 Title: Structural Insights into Pseudokinase Domains of Receptor Tyrosine Kinases. Authors: Sheetz, J.B. / Mathea, S. / Karvonen, H. / Malhotra, K. / Chatterjee, D. / Niininen, W. / Perttila, R. / Preuss, F. / Suresh, K. / Stayrook, S.E. / Tsutsui, Y. / Radhakrishnan, R. / ...Authors: Sheetz, J.B. / Mathea, S. / Karvonen, H. / Malhotra, K. / Chatterjee, D. / Niininen, W. / Perttila, R. / Preuss, F. / Suresh, K. / Stayrook, S.E. / Tsutsui, Y. / Radhakrishnan, R. / Ungureanu, D. / Knapp, S. / Lemmon, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tu9.cif.gz | 264.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tu9.ent.gz | 176.2 KB | Display | PDB format |
PDBx/mmJSON format | 6tu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/6tu9 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/6tu9 | HTTPS FTP |
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-Related structure data
Related structure data | 6tuaC 4gt4S 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: 35448.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ROR1, NTRKR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01973 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.4 Å3/Da / Density % sol: 48.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 7.2, 12% PEG20K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→42.98 Å / Num. obs: 49088 / % possible obs: 98.9 % / Redundancy: 5 % / Biso Wilson estimate: 34.75 Å2 / CC1/2: 1 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.94→1.99 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3246 / CC1/2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GT4 Resolution: 1.94→42.98 Å / SU ML: 0.2604 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 30.6522
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→42.98 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -14.0379918679 Å / Origin y: 29.2720116605 Å / Origin z: -18.6884529476 Å
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Refinement TLS group | Selection details: all |