Download MendeleyA T cell receptor peptide/MHC complex at 3.05 Angstrom resolution
Devlin, J.R., Baker, B.M., Harari, A.To be published.
6P64
Alpha-beta TCR Binding to Neoantigen KQWLVWLFL Presented by HLA-A206
- PDB DOI: https://doi.org/10.2210/pdb6P64/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Escherichia coli, Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2019-05-31 Released: 2020-06-03
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.05 Å
- R-Value Free: 0.219
- R-Value Work: 0.194
- R-Value Observed: 0.195
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MHC class I antigen | A, C [auth F] | 276 | Homo sapiens | Mutation(s): 0 Gene Names: HLA-A |  |
UniProt | |||||
Find proteins for Q53Z42 (Homo sapiens) Explore Q53Z42 Go to UniProtKB: Q53Z42 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q53Z42 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-2-microglobulin | B, D [auth G] | 100 | Homo sapiens | Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769 | |||||
PHAROS: P61769 GTEx: ENSG00000166710 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 302TIL TCR alpha chain | E [auth D], G [auth I] | 208 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 302TIL TCR beta chain | F [auth E], H [auth J] | 245 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Neoantigen peptide KQWLVWLFL | I [auth C], J [auth H] | 9 | Homo sapiens | Mutation(s): 0 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q5VTY9 (Homo sapiens) Explore Q5VTY9 Go to UniProtKB: Q5VTY9 | |||||
PHAROS: Q5VTY9 GTEx: ENSG00000054392 | |||||
Entity Groups | |||||
| UniProt Group | Q5VTY9 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | K [auth A], L [auth B], M [auth F], N [auth I], O [auth I] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.05 Å
- R-Value Free: 0.219
- R-Value Work: 0.194
- R-Value Observed: 0.195
- Space Group: P 61 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 276.641 | α = 90 |
| b = 276.641 | β = 90 |
| c = 112.465 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-06-03 Deposition Author(s): Devlin, J.R., Baker, B.M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2020-06-03
Type: Initial release - Version 1.1: 2022-03-16
Changes: Author supporting evidence, Database references - Version 1.2: 2023-10-11
Changes: Data collection, Refinement description
