+Open data
-Basic information
Entry | Database: PDB / ID: 4bgg | ||||||
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Title | Crystal structure of the ACVR1 kinase in complex with LDN-213844 | ||||||
Components | ACTIVIN RECEPTOR TYPE-1 | ||||||
Keywords | TRANSFERASE / INHIBITOR / BMP SIGNALLING | ||||||
Function / homology | Function and homology information endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition ...endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / activin receptor complex / endocardial cushion formation / smooth muscle cell differentiation / 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 / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / negative regulation of signal transduction / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / 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: 2.56 Å | ||||||
Authors | Sanvitale, C. / Canning, P. / Cooper, C. / Wang, Y. / Mohedas, A.H. / Choi, S. / Yu, P.B. / Cuny, G.D. / Nowak, R. / Coutandin, D. ...Sanvitale, C. / Canning, P. / Cooper, C. / Wang, Y. / Mohedas, A.H. / Choi, S. / Yu, P.B. / Cuny, G.D. / Nowak, R. / Coutandin, D. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Structure-Activity Relationship of 3,5-Diaryl-2-Aminopyridine Alk2 Inhibitors Reveals Unaltered Binding Affinity for Fibrodysplasia Ossificans Progressiva Causing Mutants. Authors: Mohedas, A.H. / Wang, Y. / Sanvitale, C.E. / Canning, P. / Choi, S. / Xing, X. / Bullock, A.N. / Cuny, G.D. / Yu, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bgg.cif.gz | 469.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bgg.ent.gz | 390.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/4bgg ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bgg | HTTPS FTP |
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-Related structure data
Related structure data | 3q4uS 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 oper:
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-Components
#1: Protein | Mass: 34537.633 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN, RESIDUES 201-499 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: SITE-DIRECTED MUTAGENESIS / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q04771, receptor protein serine/threonine kinase #2: Chemical | ChemComp-844 / #3: Chemical | ChemComp-FLC / #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Sequence details | CONSTITUTI | |
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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: 2.89 Å3/Da / Density % sol: 57.49 % / Description: NONE |
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Crystal grow | Details: 0.2M AMMONIUM CITRATE, 20%(W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→52.91 Å / Num. obs: 49502 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.56→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.2 / % possible all: 98.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3Q4U Resolution: 2.56→52.97 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.692 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.558 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.705 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→52.97 Å
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Refine LS restraints |
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