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- PDB-1qiv: CALMODULIN COMPLEXED WITH N-(3,3,-DIPHENYLPROPYL)-N'-[1-R-(3,4-BI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qiv | ||||||
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Title | CALMODULIN COMPLEXED WITH N-(3,3,-DIPHENYLPROPYL)-N'-[1-R-(3,4-BIS-BUTOXYPHENYL)-ETHYL]-PROPYLENEDIAMINE (DPD), 1:2 COMPLEX | ||||||
![]() | CALMODULIN | ||||||
![]() | CALCIUM-BINDING PROTEIN | ||||||
Function / homology | ![]() 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 / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / : / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / spindle microtubule / calcium-mediated signaling / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Harmat, V. / Bocskei, Z.S. / Vertessy, B.G. / Naray-Szabo, G. / Ovadi, J. | ||||||
![]() | ![]() Title: A New Potent Calmodulin Antagonist with Arylalkylamine Structure: Crystallographic, Spectroscopic and Functional Studies Authors: Harmat, V. / Bocskei, Z.S. / Naray-Szabo, G. / Bata, I. / Csutor, A.S. / Hermecz, I. / Aranyi, P. / Szabo, B. / Liliom, K. / Vertessy, B.G. / Ovadi, J. #1: ![]() Title: Simultaneous Binding of Drugs with Different Chemical Structures to Ca 2+ Calmodulin: Crystallographic and Spectroscopic Studies Authors: Vertessy, B.G. / Harmat, V. / Bocskei, Z.S. / Naray-Szabo, G. / Orosz, F. / Ovadi, J. #2: Journal: Proteins: Struct.,Funct., Genet. / Year: 1997 Title: Crystallization and Preliminary Diffraction Analysis of Ca(2+)-Calmodulin-Drug and Apocalmodulin-Drug Complexes. Authors: Vertessy, B.G. / Bocskei, Z.S. / Harmath, V. / Naray-Szabo, G. / Ovadi, J. #3: ![]() Title: Trifluoperazine-Induced Conformational Change in Ca (2+)-Calmodulin Authors: Vandonselaar, M. / Hickie, R.A. / Quail, J.W. / Delbaere, L.T.J. #4: ![]() Title: Drug Binding by Calmodulin: Crystal Structure of a Calmodulin-Trifluoperazine Complex Authors: Cook, W.J. / Walter, L.J. / Walter, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.7 KB | Display | ![]() |
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PDB format | ![]() | 30.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1qiwC ![]() 1linS S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 16721.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
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#2: Chemical | ChemComp-CA / #3: Chemical | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5 Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP TECHNIQUE AT ROOM TEMPERATURE FROM 50 MM PH=5.0 SODIUM CACODYLATE/HCL BUFFER, 10 MM MGCL2, 10 MM CACL2, 2MM DPD AND 28% PEG 8000. CRYSTAL GROWTH TOOK 2-3 WEEKS., pH 5.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: NORMAL FOCUS |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→24.58 Å / Num. obs: 4969 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.63→2.72 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 9 / % possible all: 76.2 |
Reflection | *PLUS Num. measured all: 107694 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LIN Resolution: 2.64→24.58 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 Details: DISORDERED SIDE CHAIN ATOMS OF RESIDUES ARG 74 - THR 79 AND SER 81 OF THE CENTRAL REGION, GLU 6, GLU 83, TRIMETHYL-LYSINE 115, GLU 123 AND GLU 127 ARE NOT SEEN IN THE CRYSTAL STRUCTURE, AS ...Details: DISORDERED SIDE CHAIN ATOMS OF RESIDUES ARG 74 - THR 79 AND SER 81 OF THE CENTRAL REGION, GLU 6, GLU 83, TRIMETHYL-LYSINE 115, GLU 123 AND GLU 127 ARE NOT SEEN IN THE CRYSTAL STRUCTURE, AS WELL AS THE N-TERMINAL ALA 1, ASP 2 AND C-TERMINAL ALA 147, LYS 148 RESIDUES. TEMPERATURE FACTORS FOR THE ATOMS IN RESIDUES 75 - 81 ARE UNUSUALLY HIGH, INDICATING FLEXIBILITY IN THIS REGION. THE C-TERMINAL RESIDUES WERE NOT SEEN IN THE DENSITY MAPS
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Displacement parameters | Biso mean: 28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.64→24.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.76 Å / Rfactor Rfree error: 0.085 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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