[English] 日本語
![](img/lk-miru.gif)
- PDB-1eez: Crystal Structure Determination of HLA-A2.1 Complexed to GP2 Pept... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1eez | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Determination of HLA-A2.1 Complexed to GP2 Peptide Variant(I2L/V5L) | ||||||
![]() |
| ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Sharma, A.K. / Kuhns, J.J. / Collins, E.J. | ||||||
![]() | ![]() Title: Class I major histocompatibility complex anchor substitutions alter the conformation of T cell receptor contacts. Authors: Sharma, A.K. / Kuhns, J.J. / Yan, S. / Friedline, R.H. / Long, B. / Tisch, R. / Collins, E.J. #1: ![]() Title: Poor Binding of HER-2/neu Epitope (GP2) to HLA-A2.1 is Due to a Lack of Interactions with the Center of the Peptide Authors: Kuhns, J.J. / Batalia, M.A. / Yan, S. / Collins, E.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 159.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 129.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | HLA_A2.1 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). Heavy chain is made of three sununits alpha1, alpha2 and alpha3. Peptide binds to the groove formed by the alpha1 and alpha2 domains |
-
Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-275 OF EXTRACELLULAR PORTION 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.) ![]() ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 898.142 Da / Num. of mol.: 2 / Mutation: I2L,V5L / Source method: obtained synthetically Details: The peptide was synthesized at the peptide synthesis facility of University of North Carolina at Chapel Hill. #4: Water | ChemComp-HOH / | ![]() Compound details | HLA_A2.1 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). ...HLA_A2.1 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). Heavy chain is made of three subunits alpha1, alpha2 and alpha3. Peptide binds to the groove formed by the alpha1 and alpha2 domains. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.4 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG8000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→50 Å / Num. all: 114345 / Num. obs: 33403 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 4.73 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.293 / Num. unique all: 5095 / % possible all: 84.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 114345 |
Reflection shell | *PLUS % possible obs: 84.8 % / Mean I/σ(I) obs: 2.4 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.3→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 974700.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood function
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.79 Å2 / ksol: 0.384 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|