Research workbench
Computational stabilization of T cell receptor constant domains
Analyse Computational stabilization of T cell receptor constant domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U07
- Type
- protein
- Length
- 217 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stabilized T cell receptor constant domain (calpha); Stabilized T cell receptor constant…
- UniProt
- Q2YD82, K7N5M4
- Ligands
- MG
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stabilized T cell receptor constant domain (calpha) | protein | 88 | 8% helix, 36% strand | Q2YD82 |
| B | Stabilized T cell receptor constant domain (cbeta) | protein | 129 | 9% helix, 48% strand | K7N5M4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.40 | 0.76 | 22 | empty |
| 2 | 100 | 0.40 | 0.77 | 20 | empty |
| 3 | 70 | 0.35 | 0.77 | 19 | empty |
| 4 | 65 | 0.35 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1367 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6U07 · Computational Stabilization of T Cell Receptor Constant Domains · 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
- Every structure of UniProt Q2YD82
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 6U07 · PDBe 6U07 · UniProt Q2YD82 · UniProt K7N5M4
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