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Open data
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Basic information
Entry | Database: PDB / ID: 4pd8 | ||||||
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Title | Structure of vcCNT-7C8C bound to pyrrolo-cytidine | ||||||
![]() | NupC family protein | ||||||
![]() | TRANSPORT PROTEIN / membrane protein / sodium-coupled transporter / pyrrolo-cytidine / drug transporter | ||||||
Function / homology | ![]() nucleoside transmembrane transport / nucleoside transmembrane transporter activity / pyrimidine- and adenosine-specific:sodium symporter activity / purine-specific nucleoside:sodium symporter activity / pyrimidine nucleoside transport / purine nucleoside transmembrane transport / 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 | ![]() | 91.1 KB | Display | ![]() |
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PDB format | ![]() | 65.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 893.9 KB | Display | ![]() |
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Full document | ![]() | 895.1 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pb1C ![]() 4pb2C ![]() 4pd5C ![]() 4pd6C ![]() 4pd7C ![]() 4pd9C ![]() 4pdaC ![]() 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-P0C / |
#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: 69.88 % |
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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: Aug 22, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→50 Å / Num. obs: 17711 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 64.07 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.965 / Net I/av σ(I): 22.625 / Net I/σ(I): 9.7 / Num. measured all: 103351 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TIJ Resolution: 2.75→39.16 Å / FOM work R set: 0.8168 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.69 / 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: 184.28 Å2 / Biso mean: 60.97 Å2 / Biso min: 33.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→39.16 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: 6 / % reflection obs: 100 %
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