Research workbench
D30 TCR in complex with HLA-A*11:01-GTS1
Analyse D30 TCR in complex with HLA-A*11:01-GTS1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WKF
- Type
- protein
- Length
- 1,651 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-11 alpha chain; Beta-2-microglobulin; GTS1…
- UniProt
- P13746, P61769, A0A087WSZ9, K7N5N2
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen, a-11 alpha chain | protein | 274 | 25% helix, 41% strand | P13746 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, H | GTS1 peptide | protein | 10 | 0% helix, 10% strand | — |
| D, I | T-cell receptor alpha variable 30,T-cell receptor, SP3.4 alpha chain chimera | protein | 198 | 2% helix, 43% strand | A0A087WSZ9, K7N5N2 |
| E, J | D30 TCR beta chain | protein | 244 | 7% helix, 49% strand | — |
| G | Beta-2-microglobulin | protein | 100 | 0% helix, 46% strand | P61769 |
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 | 1100 | 0.82 | 0.83 | 129 | empty |
| 2 | 888 | 0.75 | 0.79 | 71 | empty |
| 3 | 971 | 0.74 | 0.77 | 77 | empty |
| 4 | 908 | 0.72 | 0.77 | 84 | empty |
| 5 | 820 | 0.71 | 0.77 | 76 | empty |
Interfaces
20 interfaces between chains.
- I–J · 2310 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2186 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1424 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1349 Ų buried · 26 hydrogen bonds · protein-protein
- F–H · 856 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 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 P13746
- Every structure of UniProt P61769
- Every structure of UniProt A0A087WSZ9
- Every structure of UniProt K7N5N2
- Elsewhere: RCSB PDB 5WKF · PDBe 5WKF · UniProt P13746 · UniProt P61769 · UniProt A0A087WSZ9 · UniProt K7N5N2
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