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- PDB-2h26: human CD1b in complex with endogenous phosphatidylcholine and spacer -
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Open data
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Basic information
Entry | Database: PDB / ID: 2h26 | |||||||||
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Title | human CD1b in complex with endogenous phosphatidylcholine and spacer | |||||||||
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Function / homology | ![]() endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Garcia-Alles, L.F. / Maveyraud, L. / Vallina, A.T. / Guillet, V. / Mourey, L. | |||||||||
![]() | ![]() Title: Endogenous phosphatidylcholine and a long spacer ligand stabilize the lipid-binding groove of CD1b. Authors: Garcia-Alles, L.F. / Versluis, K. / Maveyraud, L. / Vallina, A.T. / Sansano, S. / Bello, N.F. / Gober, H.J. / Guillet, V. / de la Salle, H. / Puzo, G. / Mori, L. / Heck, A.J. / De Libero, G. / Mourey, L. | |||||||||
History |
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Remark 600 | HETEROGEN AUTHOR STATES THAT THIS LIGAND IS FROM UNKNOWN ENDOGENOUS LIGAND. TETRACOSYL PALMITATE ...HETEROGEN AUTHOR STATES THAT THIS LIGAND IS FROM UNKNOWN ENDOGENOUS LIGAND. TETRACOSYL PALMITATE WAS MODELLED AS PROPOSITION. THIS STRUCTURE IS PROVIDED JUST AS STARTING HYPOTHESIS. THE REAL IDENTITY OF THIS LIGAND IS A MATTER OF SPECULATION. | |||||||||
Remark 999 | SEQUENCE THE C-TERMINAL RESIDUES ON CD1B ANTIGEN, IDKLGGGLNDIFEAQKIEWHE, IS A BIRA PEPTIDE TAG. ...SEQUENCE THE C-TERMINAL RESIDUES ON CD1B ANTIGEN, IDKLGGGLNDIFEAQKIEWHE, IS A BIRA PEPTIDE TAG. HOWEVER, AMONG THE LAST 20 RESIDUES, ONLY 5 RESIDUES ARE OBSERVED. These 5 RESIDUES ARE MODELLED AS ALA AND NUMBERED 901-905. THE SEQUENCE ALIGNMENT OF THESE FIVE ALA RESIDUES ARE UNKNOWN. THESE RESIDUES ARE CHANGED TO UNK AS UNKNOWN AMINO ACIDS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.2 KB | Display | ![]() |
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PDB format | ![]() | 76.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gzpS S: Starting model for refinement |
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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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Details | the asymmetric unit contains the biological heterodimer |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31623.738 Da / Num. of mol.: 1 / Fragment: extracellular domain of CD1b antigen Mutation: BirA peptide tag (IDKLGGGLNDIFEAQKIEWHE) at C-terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Sugars , 1 types, 2 molecules
#3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 270 molecules ![](data/chem/img/6PL.gif)
![](data/chem/img/6UL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6UL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-6PL / ( | ||
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#5: Chemical | ChemComp-6UL / | ||
#6: Chemical | ChemComp-GOL / ![]() | ||
#7: Chemical | ![]() #8: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 54.5 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.5 M ammonium sulfate 5 % (v/v) isopropanol 0.1 M Na citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2005 |
Radiation | Monochromator: Khozu monochromator with dual parallel Si(111) crystals Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→32.72 Å / Num. all: 43311 / Num. obs: 43311 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5545 / Rsym value: 0.198 / % possible all: 85.5 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1GZP Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.867 / SU ML: 0.09 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.129 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.607 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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