Research workbench
TCR-peptide specificity overrides affinity enhancing TCR-MHC interactions
Analyse TCR-peptide specificity overrides affinity enhancing TCR-MHC interactions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MNQ
- Type
- protein
- Length
- 825 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; Telomerase…
- EC
- 2.7.7.49
- UniProt
- P01892, P61769, O14746, H2RG00, K7N5M9, A0A585, P01850
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 27% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 48% strand | P61769 |
| C | Telomerase reverse transcriptase (EC 2.7.7.49) | protein | 9 | 0% helix, 0% strand | O14746 |
| D | Uncharacterized protein, T-cell receptor, SP3.4 alpha chain | protein | 200 | 2% helix, 45% strand | H2RG00, K7N5M9 |
| E | V_SEGMENT translation product, T-cell receptor beta-1 chain C region | protein | 240 | 6% helix, 47% strand | A0A585, P01850 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.75 | 0.78 | 99 | empty |
| 2 | 704 | 0.70 | 0.78 | 64 | empty |
| 3 | 86 | 0.44 | 0.80 | 17 | empty |
| 4 | 95 | 0.40 | 0.77 | 17 | empty |
| 5 | 74 | 0.35 | 0.76 | 14 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2169 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1401 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 910 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 657 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 462 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4MNQ · TCR-peptide specificity overrides affinity enhancing TCR-MHC interactions · the same entry in another collection · chain E against E, 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 0.99
- P01850 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 1 (P01850) · a predicted model of the same protein · chain E against A, TM-score 0.53
- O14746 · AlphaFold monomer V2.0 prediction for telomerase reverse transcriptase (O14746) · 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 O14746
- Every structure of UniProt H2RG00
- Every structure of UniProt K7N5M9
- Every structure of UniProt A0A585
- Every structure of UniProt P01850
- Elsewhere: RCSB PDB 4MNQ · PDBe 4MNQ · UniProt P01892 · UniProt P61769 · UniProt O14746 · UniProt H2RG00 · UniProt K7N5M9 · UniProt A0A585 · UniProt P01850
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.