Research workbench
Crystal structures of high affinity human T-cell receptors bound to pmhc revealnative diagonal binding geometry TCR clone C5C1 complexed with MHC
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
- 2PYE
- Type
- protein
- Length
- 822 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61769, P78358, A2NVQ1, Q6NS87
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 27% helix, 39% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | CANCER/TESTIS antigen 1B | protein | 9 | 0% helix, 0% strand | P78358 |
| D | T-cell receptor, alpha chain | protein | 195 | 6% helix, 49% strand | A2NVQ1 |
| E | T-cell receptor, beta chain | protein | 242 | 7% helix, 48% strand | Q6NS87 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, D, E
- GOL · Glycerol · additive · 11 copies · chains A, C, D, E, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, E
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.73 | 0.76 | 105 | SO4, GOL |
| 2 | 630 | 0.68 | 0.77 | 55 | PGE, 7PE |
| 3 | 194 | 0.59 | 0.81 | 35 | GOL |
| 4 | 85 | 0.47 | 0.82 | 17 | empty |
| 5 | 189 | 0.46 | 0.75 | 32 | GOL |
Interfaces
7 interfaces between chains.
- D–E · 2040 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1374 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 818 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 451 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 346 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2PYE · 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
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P78358 · AlphaFold monomer V2.0 prediction for CANCER/TESTIS antigen 1 (P78358) · a predicted model of the same protein · chain C against A, TM-score 0.28
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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt P78358
- Every structure of UniProt A2NVQ1
- Every structure of UniProt Q6NS87
- Elsewhere: RCSB PDB 2PYE · PDBe 2PYE · UniProt P01892 · UniProt P61769 · UniProt P78358 · UniProt A2NVQ1 · UniProt Q6NS87
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