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Yorodumi- PDB-5oxg: Crystal structure of the ACVR1 (ALK2) kinase in complex with LDN-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oxg | ||||||
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Title | Crystal structure of the ACVR1 (ALK2) kinase in complex with LDN-212854 | ||||||
Components | Activin receptor type-1 | ||||||
Keywords | SIGNALING PROTEIN / Kinase / ALK2 / Receptor / BMP / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information endocardial cushion cell fate commitment / mitral valve morphogenesis / atrial septum primum morphogenesis / endocardial cushion fusion / BMP receptor complex / BMP receptor activity / cardiac muscle cell fate commitment / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition / positive regulation of determination of dorsal identity ...endocardial cushion cell fate commitment / mitral valve morphogenesis / atrial septum primum morphogenesis / endocardial cushion fusion / BMP receptor complex / BMP receptor activity / cardiac muscle cell fate commitment / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition / positive regulation of determination of dorsal identity / acute inflammatory response / transforming growth factor beta receptor activity, type I / activin receptor complex / smooth muscle cell differentiation / endocardial cushion formation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / transforming growth factor beta binding / embryonic heart tube morphogenesis / gastrulation with mouth forming second / dorsal/ventral pattern formation / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / ventricular septum morphogenesis / SMAD binding / germ cell development / positive regulation of SMAD protein signal transduction / peptide hormone binding / mesoderm formation / regulation of ossification / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of bone mineralization / negative regulation of signal transduction / protein tyrosine kinase binding / transforming growth factor beta receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / cellular response to growth factor stimulus / positive regulation of peptidyl-tyrosine phosphorylation / apical part of cell / heart development / in utero embryonic development / protein kinase activity / positive regulation of cell migration / cadherin binding / phosphorylation / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Williams, E.P. / Sorrell, F.J. / Kopec, J. / Nowak, R.P. / Kupinska, K. / von Delft, F. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Williams, E.P. / Sorrell, F.J. / Kopec, J. / Nowak, R.P. / Kupinska, K. / von Delft, F. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Bone / Year: 2018 Title: Structural basis for the potent and selective binding of LDN-212854 to the BMP receptor kinase ALK2. Authors: Williams, E. / Bullock, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oxg.cif.gz | 252.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oxg.ent.gz | 203 KB | Display | PDB format |
PDBx/mmJSON format | 5oxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/5oxg ftp://data.pdbj.org/pub/pdb/validation_reports/ox/5oxg | HTTPS FTP |
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-Related structure data
Related structure data | 3h9rS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 34537.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1, ACVRLK2 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q04771, receptor protein serine/threonine kinase #2: Chemical | ChemComp-B4B / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-EDO / | #5: 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: 2.81 Å3/Da / Density % sol: 56.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18% PEG8000 -- 0.2M calcium acetate -- 0.1M cacodylate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013 Details: Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focusing |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→65.65 Å / Num. obs: 88737 / % possible obs: 99.56 % / Observed criterion σ(F): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.052 / Rrim(I) all: 0.093 / Net I/av σ(I): 8.12 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4518 / CC1/2: 0.8 / Rpim(I) all: 0.358 / Rrim(I) all: 0.65 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H9R Resolution: 2.13→65.65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.988 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2061 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.17 / SU Rfree Cruickshank DPI: 0.1697 / Details: 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 mean: 45.974 Å2
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Refinement step | Cycle: 1 / Resolution: 2.13→65.65 Å
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Refine LS restraints |
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