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Open data
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Basic information
Entry | Database: PDB / ID: 4pda | ||||||
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Title | Structure of vcCNT-7C8C bound to cytidine | ||||||
![]() | NupC family protein | ||||||
![]() | TRANSPORT PROTEIN / membrane protein / sodium-coupled transporter / drug transporter / cytidine | ||||||
Function / homology | ![]() nucleoside transmembrane transport / nucleoside transmembrane transporter activity / symporter activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johnson, Z.L. / Lee, S.-Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters. Authors: Johnson, Z.L. / Lee, J.H. / Lee, K. / Lee, M. / Kwon, D.Y. / Hong, J. / Lee, S.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.2 KB | Display | ![]() |
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PDB format | ![]() | 65.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pb1C ![]() 4pb2C ![]() 4pd5C ![]() 4pd6C ![]() 4pd7C ![]() 4pd8C ![]() 4pd9C ![]() 3tijS 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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1 | ![]()
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Unit cell |
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Details | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 44151.848 Da / Num. of mol.: 1 / Mutation: L7C, I8C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CTN / |
#3: Chemical | ChemComp-NA / |
#4: Sugar | ChemComp-DMU / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.86 % |
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Crystal grow | Temperature: 290 K / Method: liquid diffusion / pH: 8.5 / Details: 37-42% PEG 400, 100 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 20609 / % possible obs: 99.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.145 / Net I/av σ(I): 23.95 / Net I/σ(I): 7.2 / Num. measured all: 130876 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TIJ Resolution: 2.608→48.522 Å / FOM work R set: 0.8293 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.49 / 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: 166.83 Å2 / Biso mean: 59.12 Å2 / Biso min: 33.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.608→48.522 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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