Research workbench
An affinity enhanced T cell receptor in complex with HLA-A0201 restricted HCV NS3 peptide klvalginav
Analyse An affinity enhanced T cell receptor in complex with HLA-A0201 restricted HCV… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YXU
- Type
- protein
- Length
- 1,632 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T cell receptor alpha chain; T cell receptor beta chain; HLA class I histocompatibility…
- UniProt
- P01892
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | T cell receptor alpha chain | protein | 190 | 3% helix, 42% strand | — |
| G | T cell receptor beta chain | protein | 239 | 7% helix, 46% strand | — |
| A | T cell receptor alpha chain | protein | 191 | 3% helix, 43% strand | — |
| B | T cell receptor beta chain | protein | 242 | 7% helix, 46% strand | — |
| C | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 27% helix, 39% strand | P01892 |
| D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | — |
| E | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 25% helix, 37% strand | P01892 |
| H | Beta-2-microglobulin | protein | 99 | 0% helix, 47% strand | — |
| I, J | Lys-leu-val-ala-leu-gly-ile-asn-ala-val | protein | 10 | 0% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.83 | 0.87 | 70 | empty |
| 2 | 989 | 0.77 | 0.79 | 91 | empty |
| 3 | 906 | 0.72 | 0.77 | 84 | empty |
| 4 | 651 | 0.68 | 0.77 | 56 | empty |
| 5 | 220 | 0.53 | 0.77 | 28 | empty |
Interfaces
17 interfaces between chains.
- F–G · 2379 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2317 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1400 Ų buried · 18 hydrogen bonds · protein-protein
- E–H · 1282 Ų buried · 17 hydrogen bonds · protein-protein
- E–J · 865 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5YXU · an affinity enhanced T cell receptor in complex with HLA-A0201 restricted HCV NS3 peptide… · the same entry in another collection · chain F against F, TM-score 1.00
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
- Elsewhere: RCSB PDB 5YXU · PDBe 5YXU · UniProt P01892
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