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- PDB-2euk: Crystal Structure of Human Glycolipid Transfer Protein complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2euk | ||||||
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Title | Crystal Structure of Human Glycolipid Transfer Protein complexed with 24:1 Galactosylceramide | ||||||
![]() | Glycolipid transfer protein | ||||||
![]() | LIPID TRANSPORT / Protein-glycolipid complex | ||||||
Function / homology | ![]() glycolipid transfer activity / lipid transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / Glycosphingolipid transport / glycolipid binding / intermembrane lipid transfer / response to immobilization stress ...glycolipid transfer activity / lipid transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / Glycosphingolipid transport / glycolipid binding / intermembrane lipid transfer / response to immobilization stress / lipid binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Malinina, L. / Malakhova, M.L. / Kanack, A.T. / Abagyan, R. / Brown, R.E. / Patel, D.J. | ||||||
![]() | ![]() Title: The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. Authors: Malinina, L. / Malakhova, M.L. / Kanack, A.T. / Lu, M. / Abagyan, R. / Brown, R.E. / Patel, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.6 KB | Display | ![]() |
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PDB format | ![]() | 43.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 779.6 KB | Display | ![]() |
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Full document | ![]() | 794.7 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2eumC ![]() 2evdC ![]() 2evlC ![]() 2evsC ![]() 2evtC ![]() 1sx6S 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
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/GAL.gif)
![](data/chem/img/GAL.gif)
#1: Protein | Mass: 23877.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-GAL / |
-Non-polymers , 4 types, 184 molecules ![](data/chem/img/SPH.gif)
![](data/chem/img/NER.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NER.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SPH / |
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#4: Chemical | ChemComp-NER / ( |
#5: Chemical | ChemComp-OCT / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 Details: 15-20% PEG 3350 or 8000, 50 mM potassium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 17, 2004 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. all: 18350 / Num. obs: 17855 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.049 / Χ2: 1.051 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.503 / Num. unique all: 1709 / Χ2: 1.096 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1SX6 Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.569 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.154 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.713 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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