Research workbench
Alpha-beta TCR Binding to Neoantigen KQWLVWLFL Presented by HLA-A206
Analyse Alpha-beta TCR Binding to Neoantigen KQWLVWLFL Presented by HLA-A206 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P64
- Type
- protein
- Length
- 1,629 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.05
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- MHC class I antigen; Beta-2-microglobulin; 302TIL TCR alpha chain; 302TIL TCR beta chain…
- UniProt
- U5YJP1, P61769
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · resolution 3.05 · 8 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 275 | 27% helix, 40% strand | U5YJP1 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| F | MHC class I antigen | protein | 256 | 28% helix, 34% strand | U5YJP1 |
| D | 302TIL TCR alpha chain | protein | 189 | 3% helix, 44% strand | — |
| E | 302TIL TCR beta chain | protein | 245 | 7% helix, 51% strand | — |
| I | 302TIL TCR alpha chain | protein | 202 | 3% helix, 43% strand | — |
| J | 302TIL TCR beta chain | protein | 244 | 7% helix, 51% strand | — |
| C, H | Neoantigen peptide KQWLVWLFL | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, F, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.77 | 0.79 | 92 | empty |
| 2 | 1113 | 0.71 | 0.75 | 86 | GOL |
| 3 | 1182 | 0.71 | 0.75 | 87 | empty |
| 4 | 679 | 0.69 | 0.77 | 54 | GOL |
| 5 | 465 | 0.65 | 0.78 | 34 | empty |
Interfaces
14 interfaces between chains.
- D–E · 2239 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 2237 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1438 Ų buried · 25 hydrogen bonds · protein-protein
- F–G · 1398 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 958 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6P64 · Alpha-beta TCR binding to neoantigen kqwlvwlfl presented by HLA-A206 · the same entry in another collection · chain J against J, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt U5YJP1
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6P64 · PDBe 6P64 · UniProt U5YJP1 · UniProt P61769
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