Research workbench
1E6 TCR in complex with HLA-A02 carrying mvw peptide
Analyse 1E6 TCR in complex with HLA-A02 carrying mvw peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C0A
- Type
- protein
- Length
- 1,656 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 0.82
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% 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, I | 1E6 TCR alpha chain | protein | 197 | 3% helix, 47% strand | — |
| E | 1E6 TCR beta chain | protein | 246 | 9% helix, 50% strand | — |
| J | 1E6 TCR beta chain | protein | 244 | 9% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, D, E, F, G, J
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, D, E, F, J, H, I
- GOL · Glycerol · additive · 5 copies · chains A, B, F, J, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.82 | 0.85 | 95 | empty |
| 2 | 939 | 0.76 | 0.79 | 86 | empty |
| 3 | 1183 | 0.74 | 0.77 | 92 | empty |
| 4 | 671 | 0.69 | 0.77 | 60 | SO4 |
| 5 | 654 | 0.67 | 0.76 | 64 | empty |
Interfaces
18 interfaces between chains.
- D–E · 2563 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 2281 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1345 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1342 Ų buried · 18 hydrogen bonds · protein-protein
- F–H · 906 Ų buried · 12 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 5C0A · PDBe 5C0A · UniProt P01892 · UniProt P61769
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