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Open data
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Basic information
Entry | Database: PDB / ID: 6vb2 | ||||||
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Title | HLA-B*15:02 complexed with a synthetic peptide | ||||||
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Function / homology | ![]() hydroperoxy icosatetraenoate isomerase / hepoxilin A3 synthase activity / hydroperoxy icosatetraenoate isomerase activity / intramolecular hydroxytransferase activity / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / Synthesis of 12-eicosatetraenoic acid derivatives / lipoxygenase pathway / arachidonic acid metabolic process / hepoxilin biosynthetic process ...hydroperoxy icosatetraenoate isomerase / hepoxilin A3 synthase activity / hydroperoxy icosatetraenoate isomerase activity / intramolecular hydroxytransferase activity / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / Synthesis of 12-eicosatetraenoic acid derivatives / lipoxygenase pathway / arachidonic acid metabolic process / hepoxilin biosynthetic process / ceramide biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / sphingolipid metabolic process / linoleic acid metabolic process / fat cell differentiation / establishment of skin barrier / sensory perception of pain / peroxisome proliferator activated receptor signaling pathway / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schutte, R.J. / Li, D. / Ostrov, D.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: HLA-B*15:02 complexed with a synthetic peptide Authors: Schutte, R.J. / Li, D. / Ostrov, D.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.8 KB | Display | ![]() |
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PDB format | ![]() | 79.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6uzmC ![]() 6uznC ![]() 6uzoC ![]() 6uzsC ![]() 6vb0C ![]() 6vb1C ![]() 6vb4C ![]() 6vb5C ![]() 6vb6C ![]() 6vb7C ![]() 6viuC ![]() 1xr8S 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 , 2 types, 2 molecules AB
#1: Protein | Mass: 31907.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 11388.719 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: 1169.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q9BYJ1*PLUS |
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-Non-polymers , 5 types, 482 molecules ![](data/chem/img/NA.gif)
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![](data/chem/img/ACT.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
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#4: Chemical | ChemComp-NA / | ||||||
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#5: Chemical | ![]() #6: Chemical | ![]() #7: Chemical | ChemComp-EDO / ![]() #8: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.98 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2 ammonium acetate, 0.M tri-sodium citrate dihydrate pH5.6, 30% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.36→40.17 Å / Num. obs: 93429 / % possible obs: 95.7 % / Redundancy: 1.9 % / Rrim(I) all: 0.0433 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.4→1.46 Å / Rmerge(I) obs: 0.237 / Num. unique obs: 9424 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1XR8 Resolution: 1.41→40.155 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.71 / 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: 104.73 Å2 / Biso mean: 22.2186 Å2 / Biso min: 6.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.41→40.155 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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