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- PDB-1xr8: Crystal Structures of HLA-B*1501 in Complex with Peptides from Hu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xr8 | ||||||
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Title | Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3 | ||||||
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Function / homology | ![]() host cell nuclear matrix / DNA-templated viral transcription / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roder, G. / Blicher, T. / Johannessen, B.R. / Kristensen, O. / Buus, S. / Gajhede, M. | ||||||
![]() | ![]() Title: Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype Authors: Roder, G. / Blicher, T. / Justesen, S. / Johannesen, B. / Kristensen, O. / Kastrup, J. / Buus, S. / Gajhede, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.2 KB | Display | ![]() |
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PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1xr9C ![]() 1a1mS C: citing same article ( 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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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31958.195 Da / Num. of mol.: 1 / Fragment: residues (1-276) 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.) ![]() ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1026.146 Da / Num. of mol.: 1 / Fragment: residues (274-282) / Source method: obtained synthetically / Details: chemical synthesis / References: UniProt: P12977 |
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-Non-polymers , 4 types, 229 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PG4 / ![]() | ||
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#5: Chemical | ChemComp-URE / ![]() | ||
#6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M MgAc4H20, 0.1M Na-cacodylate, pH 6.5, 20% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 28, 2004 |
Radiation | Monochromator: Bent diamond crystal, horizontally focusing (R = 12 m) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→19.44 Å / Num. all: 20977 / Num. obs: 19549 / % possible obs: 93.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 29.855 Å2 / Rsym value: 0.104 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.9 / Num. measured all: 10859 / Num. unique all: 2868 / Rsym value: 0.339 / % possible all: 96.29 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1A1M Resolution: 2.3→19.437 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.093 / SU ML: 0.152 / SU R Cruickshank DPI: 0.34 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUHGOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.975 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.437 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.35 Å / Total num. of bins used: 20
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