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- PDB-4pa0: Omecamtiv Mercarbil binding site on the Human Beta-Cardiac Myosin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pa0 | ||||||
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Title | Omecamtiv Mercarbil binding site on the Human Beta-Cardiac Myosin Motor Domain | ||||||
![]() | Myosin-7,Green fluorescent protein | ||||||
![]() | Motor/Fluorescent Protein / Cardiac / Myosin / Motor / omecamtiv mercarbil / Motor-Fluorescent Protein complex | ||||||
Function / homology | ![]() regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / myosin II complex ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / myosin II complex / myosin complex / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / microfilament motor activity / myofibril / skeletal muscle contraction / striated muscle contraction / muscle contraction / cardiac muscle contraction / stress fiber / ATP metabolic process / regulation of heart rate / sarcomere / bioluminescence / generation of precursor metabolites and energy / Z disc / actin filament binding / calmodulin binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Winkelmann, D.A. / Miller, M.T. / Stock, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for drug-induced allosteric changes to human beta-cardiac myosin motor activity. Authors: Winkelmann, D.A. / Forgacs, E. / Miller, M.T. / Stock, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 389.9 KB | Display | ![]() |
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PDB format | ![]() | 308.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4p7hS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | monomer in solution based on gel filtration |
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Components
#1: Protein | Mass: 116609.812 Da / Num. of mol.: 2 Fragment: UNP P12883 residues 1-787, UNP P42212 residues 5-234 Mutation: Q80R, V163A, I167T, S175G, D190N Source method: isolated from a genetically manipulated source Details: cloned cDNA Source: (gene. exp.) ![]() ![]() ![]() Tissue: muscle / Cell: cardiomyocyte / Gene: MYH7, MYHCB, GFP / Organ: Heart Details (production host): replication defective adenovirus infection Cell (production host): myoblast / Cell line (production host): C2C12 cells / Organ (production host): skeletal muscle / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | YKDHD are a minimal Flag epitope tag engineered into the sequence to facilitate purification by the author | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.4 % / Description: small orthorhombic crystals, green in color |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Tacsimate, pH 6.0, PEG 3350, glycerol, MgCL2, TCEP and ligand, omecamptiv mercarbil PH range: 5.8-6.4 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: crystals cryopreserved in mother liquor |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2014 |
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→46.042 Å / Num. obs: 106961 / % possible obs: 93.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.499 / Mean I/σ(I) obs: 0.8 / % possible all: 84 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4P7H Resolution: 2.25→45.961 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.84 / 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: 2.25→45.961 Å
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Refine LS restraints |
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LS refinement shell |
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