Research workbench
Mouse diabetogenic TCR 8F10
Analyse Mouse diabetogenic TCR 8F10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DFV
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TCR alpha chain; TCR beta chain
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TCR alpha chain | protein | 190 | 4% helix, 44% strand | — |
| B, D | TCR beta chain | protein | 240 | 7% helix, 50% strand | — |
| C | TCR alpha chain | protein | 200 | 3% helix, 43% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.77 | 0.79 | 91 | empty |
| 2 | 974 | 0.76 | 0.79 | 73 | empty |
| 3 | 1176 | 0.76 | 0.78 | 120 | empty |
| 4 | 123 | 0.45 | 0.77 | 25 | empty |
| 5 | 82 | 0.40 | 0.78 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2184 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2160 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 546 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 536 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 96 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6DFV · Mouse diabetogenic TCR 8F10 · 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 6DFV · PDBe 6DFV
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