+Open data
-Basic information
Entry | Database: PDB / ID: 6ke5 | ||||||
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Title | Structure of CavAb in complex with Diltiazem and Amlodipine | ||||||
Components | Ion transport protein | ||||||
Keywords | MEMBRANE PROTEIN / Voltage gated Ion Channel / Voltage-gated Calcium Channel / Block / Tetrameric | ||||||
Function / homology | Function and homology information voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Arcobacter butzleri RM4018 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å | ||||||
Authors | Tang, L. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2019 Title: Structural Basis for Diltiazem Block of a Voltage-Gated Ca2+Channel. Authors: Tang, L. / Gamal El-Din, T.M. / Lenaeus, M.J. / Zheng, N. / Catterall, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ke5.cif.gz | 202.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ke5.ent.gz | 160.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ke5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ke5_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 6ke5_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 6ke5_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 6ke5_validation.cif.gz | 57 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/6ke5 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/6ke5 | HTTPS FTP |
-Related 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, 4 molecules ABCD
#1: Protein | Mass: 32957.766 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri RM4018 (bacteria) / Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5 |
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-Non-polymers , 6 types, 14 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-G3P / #5: Chemical | ChemComp-6UB / | #6: Chemical | ChemComp-D6C / [( | #7: Water | ChemComp-HOH / | |
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-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: 5.67 Å3/Da / Density % sol: 78.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Na-citrate,pH5.0,2M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→44.706 Å / Num. obs: 66929 / % possible obs: 90.8 % / Redundancy: 4.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 9478 / CC1/2: 0.861 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.803→44.706 Å / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.48 / Stereochemistry target values: TWIN_LSQ_F
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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: 244.37 Å2 / Biso mean: 80.8363 Å2 / Biso min: 20.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.803→44.706 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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