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Open data
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Basic information
Entry | Database: PDB / ID: 5kmf | |||||||||
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Title | Structure of CavAb in complex with nimodipine | |||||||||
![]() | Ion transport protein | |||||||||
![]() | TRANSPORT PROTEIN / Voltage-gated Calcium Channel | |||||||||
Function / homology | ![]() membrane depolarization during action potential / voltage-gated sodium channel complex / voltage-gated sodium channel activity / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tang, L. / Gamal EL-Din, T.M. / Swanson, T.M. / Pryde, D.C. / Scheuer, T. / Zheng, N. / Catterall, W.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for inhibition of a voltage-gated Ca(2+) channel by Ca(2+) antagonist drugs. Authors: Tang, L. / El-Din, T.M. / Swanson, T.M. / Pryde, D.C. / Scheuer, T. / Zheng, N. / Catterall, W.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 394.6 KB | Display | ![]() |
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PDB format | ![]() | 322.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5klbC ![]() 5klgC ![]() 5klsC ![]() 5kmdC ![]() 5kmhC ![]() 4ms2S 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: 33088.965 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RM4018 / Gene: Abu_1752 / Plasmid: pFASTBAC DUAL / Production host: ![]() #2: Chemical | ChemComp-6U9 / | #3: Chemical | ChemComp-MC3 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.68 Å3/Da / Density % sol: 78.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate,100uM nimodipine PH range: 4.7-5.3 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9199 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.2→30 Å / Num. obs: 55285 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.2 | |||||||||||||||
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 9 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MS2 Resolution: 3.2→29.79 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.911 / SU B: 22.014 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 105.829 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→29.79 Å
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Refine LS restraints |
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