Research workbench
p53-specific T cell receptor
Analyse p53-specific T cell receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VTH
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.36
- Source
- Homo sapiens
- Molecule
- T-cell Receptor 12-6, Alfa chain; TCR 12-6, beta chain
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.36 · 4 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell Receptor 12-6, Alfa chain | protein | 192 | 5% helix, 47% strand | — |
| B | TCR 12-6, beta chain | protein | 240 | 8% helix, 50% strand | — |
| D | T-cell Receptor 12-6, Alfa chain | protein | 193 | 5% helix, 46% strand | — |
| E | TCR 12-6, beta chain | protein | 242 | 7% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.72 | 0.76 | 79 | empty |
| 2 | 975 | 0.71 | 0.75 | 77 | empty |
| 3 | 147 | 0.54 | 0.81 | 25 | empty |
| 4 | 264 | 0.47 | 0.73 | 39 | empty |
| 5 | 77 | 0.39 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2129 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2119 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 350 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6VTH · P53-specific T cell receptor · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6VTH · PDBe 6VTH
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