Research workbench
1E6 TCR in complex with HLA-A02 carrying yqfgpdfpia
Analyse 1E6 TCR in complex with HLA-A02 carrying yqfgpdfpia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C07
- Type
- protein
- Length
- 1,663 residues
- Chains
- 10
- 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; Marker…
- UniProt
- P01892, P61769
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 41% strand | P01892 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, H | Marker peptide | protein | 10 | 0% helix, 0% strand | — |
| D, I | 1E6 TCR alpha chain | protein | 199 | 2% helix, 41% strand | — |
| E, J | 1E6 TCR beta chain | protein | 246 | 7% helix, 50% strand | — |
| F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 277 | 25% helix, 40% strand | P01892 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, D, F, I, J
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, D, E, C, F, G, I, J
- GOL · Glycerol · additive · 7 copies · chains F, J, H, I, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.76 | 0.78 | 94 | empty |
| 2 | 983 | 0.75 | 0.78 | 90 | empty |
| 3 | 705 | 0.70 | 0.77 | 73 | empty |
| 4 | 622 | 0.68 | 0.77 | 57 | empty |
| 5 | 333 | 0.66 | 0.81 | 52 | GOL, EDO |
Interfaces
17 interfaces between chains.
- I–J · 2415 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2374 Ų buried · 31 hydrogen bonds · protein-protein
- F–G · 1398 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1326 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 875 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5C07 · PDBe 5C07 · UniProt P01892 · UniProt P61769
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