Research workbench
Mouse diabetogenic TCR I.29
Analyse Mouse diabetogenic TCR I.29 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DFQ
- Type
- protein
- Length
- 1,709 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TCR alpha chain; TCR beta chain
- Ligands
- CA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | TCR alpha chain | protein | 199 | 3% helix, 47% strand | — |
| F | TCR beta chain | protein | 238 | 5% helix, 54% strand | — |
| A | TCR alpha chain | protein | 195 | 2% helix, 47% strand | — |
| B | TCR beta chain | protein | 239 | 5% helix, 54% strand | — |
| C | TCR alpha chain | protein | 200 | 2% helix, 47% strand | — |
| D | TCR beta chain | protein | 237 | 5% helix, 55% strand | — |
| G | TCR alpha chain | protein | 167 | 2% helix, 51% strand | — |
| H | TCR beta chain | protein | 234 | 5% helix, 55% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.75 | 0.79 | 95 | EDO |
| 2 | 1065 | 0.74 | 0.77 | 95 | empty |
| 3 | 1132 | 0.73 | 0.76 | 83 | empty |
| 4 | 1069 | 0.72 | 0.76 | 80 | empty |
| 5 | 787 | 0.72 | 0.77 | 62 | empty |
Interfaces
13 interfaces between chains.
- E–F · 2157 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2144 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2097 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1833 Ų buried · 17 hydrogen bonds · protein-protein
- E–C · 687 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide (disulfide).
Compared structures
- 6DFQ · mouse diabetogenic TCR I.29 · the same entry in another collection · chain E against E, 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 6DFQ · PDBe 6DFQ
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