Research workbench
The complex between TCR A6 and human class I MHC HLA-A2 with the modified HTLV-1 tax (Y5(4-fluorophenylalanine)) 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
- 3D39
- 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
- 9 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 25% helix, 42% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Modified HTLV-1 tax (Y5(4FLUORO)F) peptide | protein | 9 | 0% helix, 0% strand | — |
| D | A6 TCR alpha chain | protein | 200 | 4% helix, 46% strand | — |
| E | A6 TCR beta chain | protein | 245 | 7% helix, 48% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.72 | 0.76 | 86 | GOL |
| 2 | 700 | 0.69 | 0.77 | 58 | empty |
| 3 | 123 | 0.49 | 0.80 | 28 | empty |
| 4 | 118 | 0.47 | 0.79 | 22 | empty |
| 5 | 85 | 0.45 | 0.80 | 16 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2239 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1369 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 859 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 254 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 3D39 · 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 3D39 · PDBe 3D39 · UniProt P01892 · UniProt P61769
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