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(27-35)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
- 6D78
- Type
- protein
- Length
- 809 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, K7N5M3, K7N5M4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 27% helix, 42% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Melanoma antigen recognized by T-cells 1 | protein | 9 | 0% helix, 0% strand | Q16655 |
| D | DMF5 alpha CHAIN,DMF5 alpha chain | protein | 185 | 2% helix, 48% strand | K7N5M3 |
| E | DMF5 beta CHAIN,DMF5 beta chain | protein | 240 | 7% helix, 49% strand | K7N5M4 |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.73 | 0.76 | 88 | empty |
| 2 | 580 | 0.67 | 0.77 | 63 | empty |
| 3 | 125 | 0.49 | 0.79 | 22 | empty |
| 4 | 58 | 0.48 | 0.85 | 20 | empty |
| 5 | 57 | 0.43 | 0.83 | 17 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2275 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1493 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 747 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 606 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 437 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6D78 · 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 0.98
- 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 0.30
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
- Every structure of UniProt K7N5M3
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 6D78 · PDBe 6D78 · UniProt P01892 · UniProt P61769 · UniProt Q16655 · UniProt K7N5M3 · UniProt K7N5M4
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