Research workbench
1E6 TCR in complex with HLA-A0E carrying rqwgpdpaav
Analyse 1E6 TCR in complex with HLA-A0E carrying rqwgpdpaav in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C08
- Type
- protein
- Length
- 1,641 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 0.81
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 25% helix, 39% 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 | 1E6 TCR alpha chain | protein | 189 | 2% helix, 47% strand | — |
| E | 1E6 TCR beta chain | protein | 244 | 7% helix, 50% strand | — |
| I | 1E6 TCR alpha chain | protein | 191 | 2% helix, 46% strand | — |
| J | 1E6 TCR beta chain | protein | 245 | 9% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains D, A, E, F, J
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B, C, E, D, F, H, J, G, I
- GOL · Glycerol · additive · 3 copies · chains A, B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.81 | 0.83 | 95 | EDO |
| 2 | 1027 | 0.76 | 0.78 | 100 | empty |
| 3 | 797 | 0.74 | 0.79 | 84 | empty |
| 4 | 644 | 0.68 | 0.77 | 67 | EDO |
| 5 | 645 | 0.68 | 0.77 | 61 | GOL |
Interfaces
18 interfaces between chains.
- I–J · 2249 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 2202 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1394 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1382 Ų buried · 18 hydrogen bonds · protein-protein
- F–H · 873 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
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 5C08 · PDBe 5C08 · UniProt P01892 · UniProt P61769
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