MolNFT v1 · #36418 · protein
Directed evolution of human T-cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without apparent cross-reactivity
2F53 · HLA class I histocompatibility antigen: “Directed evolution of human T-cell receptor CDR2 residues by phage display dramatically enhances affinity for…”. X-ray diffraction, 1 ligand (NA), 9 pockets (best druggability 0.73). MolNFT…
- PDB
- 2F53
- Type
- protein
- Length
- 820 residues
- Chains
- 5
- 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
- Ligands
- NA
- 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 | protein | 275 | 28% 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 | 193 | 5% helix, 49% strand | Q6PIZ8 |
| E | T-cell receptor, beta chain | protein | 243 | 7% helix, 50% strand | — |
Ligands and binding sites
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 | 1152 | 0.73 | 0.76 | 100 | empty |
| 2 | 650 | 0.68 | 0.77 | 65 | GOL |
| 3 | 172 | 0.52 | 0.78 | 25 | empty |
| 4 | 51 | 0.48 | 0.86 | 17 | empty |
| 5 | 139 | 0.46 | 0.78 | 29 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2067 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1366 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 820 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 498 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 334 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 2F53 · Directed Evolution of Human T-cell Receptor CDR2 residues by phage display dramatically… · 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 0.97
- 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 0.41
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
- Elsewhere: RCSB PDB 2F53 · PDBe 2F53 · UniProt P01892 · UniProt P61769 · UniProt P78358 · UniProt Q6PIZ8
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