Research workbench
Crystal structures of high affinity human T-cell receptors bound to pmhc revealnative diagonal binding geometry unbound TCR clone 5-1
Analyse Crystal structures of high affinity human T-cell receptors bound to pmhc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PYF
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell receptor, alpha chain; T-cell receptor, beta chain
- UniProt
- Q6PIZ8, Q6NS87
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell receptor, alpha chain | protein | 205 | 5% helix, 48% strand | Q6PIZ8 |
| B | T-cell receptor, beta chain | protein | 241 | 7% helix, 51% strand | Q6NS87 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- PGE · Triethylene glycol · additive · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.73 | 0.76 | 85 | PG4, SO4 |
| 2 | 98 | 0.41 | 0.77 | 22 | PGE |
| 3 | 103 | 0.38 | 0.75 | 23 | empty |
| 4 | 95 | 0.34 | 0.74 | 16 | empty |
| 5 | 54 | 0.32 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2359 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2PYF · Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative… · the same entry in another collection · chain B against B, 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 Q6PIZ8
- Every structure of UniProt Q6NS87
- Elsewhere: RCSB PDB 2PYF · PDBe 2PYF · UniProt Q6PIZ8 · UniProt Q6NS87
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