Research workbench
D30 TCR in complex with HLA-A*11:01-GTS3
Analyse D30 TCR in complex with HLA-A*11:01-GTS3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WKH
- 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; GTS3…
- UniProt
- P13746, P61769, A0A087WSZ9, K7N5N2
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen, a-11 alpha chain | protein | 274 | 25% helix, 39% strand | P13746 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 47% strand | P61769 |
| C, H | GTS3 peptide | protein | 10 | 0% helix, 10% strand | — |
| D, I | T-cell receptor alpha variable 30,T-cell receptor, SP3.4 alpha chain | protein | 198 | 0% helix, 45% 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.82 | 0.84 | 130 | empty |
| 2 | 937 | 0.75 | 0.78 | 89 | empty |
| 3 | 1051 | 0.73 | 0.76 | 80 | empty |
| 4 | 483 | 0.69 | 0.80 | 50 | empty |
| 5 | 658 | 0.69 | 0.77 | 52 | empty |
Interfaces
20 interfaces between chains.
- I–J · 2353 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 2246 Ų buried · 29 hydrogen bonds · protein-protein
- F–G · 1380 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1345 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 860 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 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 5WKH · PDBe 5WKH · UniProt P13746 · UniProt P61769 · UniProt A0A087WSZ9 · UniProt K7N5N2
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