Research workbench
Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*01- sllmwitqv
Analyse Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*01- sllmwitqv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RPA
- Type
- protein
- Length
- 785 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61769
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 27% helix, 37% strand | P01892 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Heteroclitic ny-eso-1 157-165 peptide | protein | 9 | 0% helix, 0% strand | — |
| D | T-cell receptor alpha chain | protein | 166 | 2% helix, 46% strand | — |
| E | T-cell receptor beta chain | protein | 235 | 8% helix, 48% strand | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.70 | 0.78 | 63 | empty |
| 2 | 692 | 0.66 | 0.75 | 66 | empty |
| 3 | 164 | 0.55 | 0.81 | 18 | empty |
| 4 | 97 | 0.46 | 0.80 | 21 | empty |
| 5 | 91 | 0.42 | 0.78 | 21 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2034 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1310 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 834 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 613 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6RPA · Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*01-SLLMWITQV · the same entry in another collection · chain A against A, 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6RPA · PDBe 6RPA · UniProt P01892 · UniProt P61769
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