Research workbench
Preservation of peptide specificity during TCR-MHC contact dominated affinity enhancement of a melanoma-specific TCR
Analyse Preservation of peptide specificity during TCR-MHC contact dominated affinity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JFF
- Type
- protein
- Length
- 828 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; Melanoma…
- UniProt
- P01892, P61769
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 25% helix, 39% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 48% strand | P61769 |
| C | Melanoma motif | protein | 10 | 0% helix, 10% strand | — |
| D | High affinity TCR alpha chain | protein | 197 | 2% helix, 47% strand | — |
| E | High affinity TCR beta chain | protein | 245 | 7% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, E, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.72 | 0.76 | 91 | empty |
| 2 | 572 | 0.66 | 0.77 | 58 | empty |
| 3 | 105 | 0.46 | 0.79 | 21 | empty |
| 4 | 87 | 0.44 | 0.80 | 19 | SO4 |
| 5 | 92 | 0.40 | 0.77 | 23 | EPE |
Interfaces
7 interfaces between chains.
- D–E · 2222 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1458 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 896 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 583 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 570 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4JFF · Preservation of peptide specificity during TCR-MHC contact dominated affinity enhancement… · 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 0.98
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
- Elsewhere: RCSB PDB 4JFF · PDBe 4JFF · UniProt P01892 · UniProt P61769
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