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Structure and binding kinetics of three different human CD1D-alpha-galactosylceramide-specific T cell receptors (TCR 5E)
Analyse Structure and binding kinetics of three different human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CDF
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TCR 5E
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TCR 5E | protein | 191 | 5% helix, 48% strand | — |
| B | TCR 5E | protein | 244 | 7% helix, 49% strand | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.71 | 0.75 | 87 | empty |
| 2 | 85 | 0.49 | 0.82 | 19 | empty |
| 3 | 104 | 0.42 | 0.77 | 22 | empty |
| 4 | 82 | 0.32 | 0.74 | 19 | empty |
| 5 | 58 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2122 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2CDF · Structure and binding kinetics of three different human CD1d-alpha… · 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 2CDF · PDBe 2CDF
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