Research workbench
The complex between TCR A6 and human class I MHC HLA-A2 with the modified HTLV-1 tax (Y5(3,4-difluorophenylalanine)) peptide
Analyse The complex between TCR A6 and human class I MHC HLA-A2 with the modified… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D3V
- Type
- protein
- Length
- 829 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; Modified…
- UniProt
- P01892, P61769
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 24% helix, 39% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 50% strand | P61769 |
| C | Modified HTLV-1 tax (Y5(3,4-DIFLUORO)F) peptide | protein | 9 | 0% helix, 0% strand | — |
| D | A6 TCR alpha chain | protein | 200 | 2% helix, 41% strand | — |
| E | A6 TCR beta chain | protein | 245 | 6% helix, 49% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.70 | 0.75 | 74 | GOL |
| 2 | 491 | 0.66 | 0.78 | 45 | empty |
| 3 | 94 | 0.48 | 0.81 | 18 | empty |
| 4 | 105 | 0.41 | 0.77 | 18 | empty |
| 5 | 76 | 0.37 | 0.78 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2298 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1401 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 269 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 3D3V · The complex between TCR A6 and human Class I MHC HLA-A2 with the modified HTLV-1 TAX… · 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 3D3V · PDBe 3D3V · UniProt P01892 · UniProt P61769
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