Research workbench
Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity
Analyse Directed evolution of human T cell receptor CDR2 residues by phage display… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F54
- Type
- protein
- Length
- 1,659 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen; Beta-2-microglobulin; CANCER/TESTIS antigen 1B…
- UniProt
- P01892, P61769, P78358, Q6PIZ8, Q6NS87
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen | protein | 274 | 25% helix, 38% strand | P01892 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, H | CANCER/TESTIS antigen 1B | protein | 9 | 0% helix, 0% strand | P78358 |
| D | T-cell receptor alpha chain | protein | 205 | 4% helix, 47% strand | Q6PIZ8 |
| E, L | T-cell receptor beta chain | protein | 241 | 6% helix, 48% strand | Q6NS87 |
| K | T-cell receptor alpha chain | protein | 206 | 4% helix, 46% strand | Q6PIZ8 |
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.71 | 0.75 | 104 | empty |
| 2 | 941 | 0.70 | 0.75 | 90 | empty |
| 3 | 622 | 0.67 | 0.77 | 60 | empty |
| 4 | 564 | 0.66 | 0.77 | 54 | empty |
| 5 | 118 | 0.52 | 0.82 | 19 | empty |
Interfaces
14 interfaces between chains.
- K–L · 2217 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2187 Ų buried · 29 hydrogen bonds · protein-protein
- F–G · 1312 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1285 Ų buried · 25 hydrogen bonds · protein-protein
- F–H · 825 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 2F54 · Directed evolution of human T cell receptor CDR2 residues by phage display dramatically… · the same entry in another collection · chain L against L, 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 0.97
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 Q6PIZ8
- Every structure of UniProt Q6NS87
- Elsewhere: RCSB PDB 2F54 · PDBe 2F54 · UniProt P01892 · UniProt P61769 · UniProt P78358 · UniProt Q6PIZ8 · UniProt Q6NS87
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