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- PDB-7nmd: Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nmd | ||||||
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Title | Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL | ||||||
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Function / homology | ![]() positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rizkallah, P.J. / Sewell, A.K. / Cole, D.K. | ||||||
![]() | ![]() Title: Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL Authors: Rizkallahp, P.J. / Sewell, A.K. / Cole, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.4 KB | Display | ![]() |
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PDB format | ![]() | 273.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2bckS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 31778.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 1097.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 4 types, 259 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / ![]() #5: Chemical | ChemComp-PEG / ![]() #6: Chemical | ChemComp-SO4 / ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.18 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 0.1 M TRIS (pH 7.5), 15% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 17, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→74.01 Å / Num. obs: 43149 / % possible obs: 99 % / Redundancy: 3.7 % / CC1/2: 0.984 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.089 / Rrim(I) all: 0.174 / Net I/σ(I): 5.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2BCK Resolution: 2.25→74.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 21.485 / SU ML: 0.244 / SU R Cruickshank DPI: 0.3268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 132.07 Å2 / Biso mean: 47.57 Å2 / Biso min: 24.33 Å2
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Refinement step | Cycle: final / Resolution: 2.25→74.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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