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Yorodumi- PDB-4rjd: TFP bound in alternate orientations to calcium-saturated Calmodul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rjd | ||||||
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Title | TFP bound in alternate orientations to calcium-saturated Calmodulin C-Domains | ||||||
Components | Calmodulin | ||||||
Keywords | Calcium-Binding Protein / anti-psychotic / antagonist / Ca2+ binding / central nervous system / Trifluoromethyl / promiscuous binding / TFP-binding | ||||||
Function / homology | Function and homology information regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / calcium channel regulator activity / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / potassium ion transmembrane transport / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / cellular response to type II interferon / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / disordered domain specific binding / myelin sheath / growth cone / vesicle / transmembrane transporter binding / protein autophosphorylation / neuron projection / positive regulation of apoptotic process / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Feldkamp, M.D. / Gakhar, L. / Pandey, N. / Shea, M.A. | ||||||
Citation | Journal: Proteins / Year: 2015 Title: Opposing orientations of the anti-psychotic drug trifluoperazine selected by alternate conformations of M144 in calmodulin. Authors: Feldkamp, M.D. / Gakhar, L. / Pandey, N. / Shea, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rjd.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rjd.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 4rjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rjd_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4rjd_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4rjd_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 4rjd_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/4rjd ftp://data.pdbj.org/pub/pdb/validation_reports/rj/4rjd | HTTPS FTP |
-Related structure data
Related structure data | 1linS S: Starting model for refinement |
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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: 7608.289 Da / Num. of mol.: 2 / Fragment: Calmodulin C-Domian, UNP residues 83-148 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc Production host: Escherichia coli (E. coli) / Strain (production host): E.Coli BL21 (DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS |
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-Non-polymers , 7 types, 93 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-TFP / #4: Chemical | ChemComp-1PE / | #5: Chemical | #6: Chemical | ChemComp-OXL / | #7: Chemical | ChemComp-SCN / | #8: 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: 2.44 Å3/Da / Density % sol: 49.67 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 50 mM HEPES, 100 mM KCl, 1mM MgCl2, 5 mM NTA, 50 uM EGTA, with 500 ul of 200 mM potassium thiocyanate, 20% polyethylene glycol 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jun 14, 2007 / Details: Mirror |
Radiation | Monochromator: Rosenbaum-Rock Si(111) sagitally focused / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.23 Å / Num. obs: 8955 / % possible obs: 90.45 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 21.02 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 8.1 / Num. unique all: 1367 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LIN Resolution: 2→27.23 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 29.61 / 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→27.23 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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