Research workbench
Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms
Analyse Structural features underlying T-cell receptor sensitivity to concealed MHC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YPL
- Type
- protein
- Length
- 821 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-57 alpha chain; Beta-2-microglobulin; KF11 P24…
- UniProt
- P18465, P61769
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-57 alpha chain | protein | 274 | 28% helix, 39% strand | P18465 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | KF11 P24 gag peptide | protein | 11 | 0% helix, 0% strand | — |
| D | Aga T-cell receptor alpha chain | protein | 199 | 5% helix, 45% strand | — |
| E | Aga T-cell receptor beta chain | protein | 238 | 6% helix, 49% strand | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.76 | 0.81 | 83 | empty |
| 2 | 578 | 0.70 | 0.79 | 55 | empty |
| 3 | 856 | 0.69 | 0.75 | 77 | empty |
| 4 | 54 | 0.48 | 0.85 | 18 | empty |
| 5 | 141 | 0.47 | 0.77 | 27 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2158 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1299 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 887 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 405 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 305 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2YPL · Structural features underlying T-cell receptor sensitivity to concealed MHC class I… · 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 0.99
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 P18465
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 2YPL · PDBe 2YPL · UniProt P18465 · UniProt P61769
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