+Open data
-Basic information
Entry | Database: PDB / ID: 6v3c | ||||||
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Title | K2P2.1(TREK-1)I110D:Ru360 bound channel structure | ||||||
Components | Potassium channel subfamily K member 2 | ||||||
Keywords | MEMBRANE PROTEIN / K channel / TREK-1 / Mus musculus | ||||||
Function / homology | Function and homology information TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity / outward rectifier potassium channel activity ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity / outward rectifier potassium channel activity / negative regulation of DNA biosynthetic process / cochlea development / voltage-gated potassium channel activity / calyx of Held / response to axon injury / voltage-gated potassium channel complex / axon terminus / response to mechanical stimulus / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / memory / cellular response to hypoxia / apical plasma membrane / G protein-coupled receptor signaling pathway / axon / neuronal cell body / cell surface / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å | ||||||
Authors | Pope, L. / Lolicato, M. / Minor, D.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Chem Biol / Year: 2020 Title: Polynuclear Ruthenium Amines Inhibit K2PChannels via a "Finger in the Dam" Mechanism. Authors: Pope, L. / Lolicato, M. / Minor Jr., D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v3c.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v3c.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 6v3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/6v3c ftp://data.pdbj.org/pub/pdb/validation_reports/v3/6v3c | HTTPS FTP |
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-Related structure data
Related structure data | 6v36C 6v37C 6v3iC 4rueS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34305.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Komagataella pastoris (fungus) / References: UniProt: P97438*PLUS |
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-Non-polymers , 7 types, 17 molecules
#2: Chemical | ChemComp-RU3 / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-OCT / #6: Chemical | ChemComp-LNK / | #7: Chemical | ChemComp-HEX / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 3.79 Å3/Da / Density % sol: 67.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M KCl, 1-3 mM CdCl2, 0.1 M HEPES 7-8, 20-25% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.51→46.4 Å / Num. obs: 12595 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 3.51→3.85 Å / Num. unique obs: 530 / CC1/2: 0.149 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RUE Resolution: 3.51→14.98 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 44.65 / 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 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 327.88 Å2 / Biso mean: 203.5724 Å2 / Biso min: 119.59 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.51→14.98 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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