Research workbench
The complex between high affinity TCR DMF5(ALPHA-D26Y,BETA-L98W) and human class I MHC HLA-A2 with the bound mart-1(26-35)(A27L) peptide
Analyse The complex between high affinity TCR DMF5(ALPHA-D26Y,BETA-L98W) and human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L3E
- Type
- protein
- Length
- 826 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, Q16655
- Pockets
- 8 · best druggability 0.72
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 | 275 | 25% helix, 39% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C | Melanoma antigen recognized by T-cells 1 | protein | 10 | 0% helix, 0% strand | Q16655 |
| D | DMF5 alpha chain | protein | 199 | 2% helix, 44% strand | — |
| E | DMF5 beta chain | protein | 242 | 7% helix, 48% strand | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.72 | 0.76 | 85 | empty |
| 2 | 625 | 0.69 | 0.77 | 60 | empty |
| 3 | 104 | 0.53 | 0.83 | 18 | empty |
| 4 | 116 | 0.47 | 0.79 | 18 | empty |
| 5 | 140 | 0.46 | 0.77 | 22 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2198 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1351 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 902 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 668 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 431 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 4L3E · The complex between high affinity TCR DMF5(alpha-D26Y,beta-L98W) and human Class I MHC… · 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
- Q16655 · AlphaFold monomer V2.0 prediction for melanoma antigen recognized by T-cells 1 (Q16655) · 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 Q16655
- Elsewhere: RCSB PDB 4L3E · PDBe 4L3E · UniProt P01892 · UniProt P61769 · UniProt Q16655
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