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Open data
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Basic information
Entry | Database: PDB / ID: 2jcc | ||||||
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Title | AH3 recognition of mutant HLA-A2 W167A | ||||||
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Function / homology | ![]() Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / PD-1 signaling / Generation of second messenger molecules / tail-anchored membrane protein insertion into ER membrane / Downstream TCR signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miller, P. / Benhar, Y.P. / Biddison, W. / Collins, E.J. | ||||||
![]() | ![]() Title: Single Mhc Mutation Eliminates Enthalpy Associated with T Cell Receptor Binding. Authors: Miller, P. / Pazy, Y. / Conti, B. / Riddle, D. / Appella, E. / Collins, E.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 331.2 KB | Display | ![]() |
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PDB format | ![]() | 267 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2j8uC ![]() 2uweC ![]() 1lp9S 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 , 4 types, 8 molecules AHBIELFM
#1: Protein | Mass: 31739.070 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 25-299 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Protein | Mass: 21656.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #5: Protein | Mass: 26890.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Protein/peptide / Non-polymers , 2 types, 56 molecules CJ![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 1049.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Compound details | ENGINEEREDSequence details | MUTATION W167A | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 40.7 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 1, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→30 Å / Num. obs: 152000 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.5→2.67 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 85 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1LP9 Resolution: 2.5→122.17 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 31.854 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 0.88 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS IN THE TCR VALPHA CHAINS 50-60 ARE GIVEN ZERO OCCUPANCIES. THERE ARE TWO COMPLEXES IN THE AU. A,B,C,E,F ARE DUPLICATED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS IN THE TCR VALPHA CHAINS 50-60 ARE GIVEN ZERO OCCUPANCIES. THERE ARE TWO COMPLEXES IN THE AU. A,B,C,E,F ARE DUPLICATED AS H,I,J,L,M RESPECTIVELY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→122.17 Å
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Refine LS restraints |
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