MolNFT v1 · #76245 · protein
The complex between TCR DMF4 and human class I MHC HLA-A2 with the bound mart-1(27-35) nonameric peptide
3QEQ · HLA class I histocompatibility antigen, a-2 alpha chain: “The complex between TCR DMF4 and human class I MHC HLA-A2 with the bound mart-1(27-35) nonameric peptide”. X-ray diffraction, 10 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 3QEQ
- Type
- protein
- Length
- 821 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…
- UniProt
- P01892, P61769
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 12% 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, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Mart-1(27-35) peptide | protein | 9 | 0% helix, 22% strand | — |
| D | DMF4 alpha chain | protein | 194 | 3% helix, 45% strand | — |
| E | DMF4 beta chain | protein | 243 | 7% helix, 53% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.71 | 0.75 | 74 | empty |
| 2 | 661 | 0.70 | 0.78 | 56 | empty |
| 3 | 320 | 0.60 | 0.78 | 51 | empty |
| 4 | 137 | 0.43 | 0.76 | 29 | empty |
| 5 | 91 | 0.43 | 0.79 | 21 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2147 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1369 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 774 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 476 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 468 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3QEQ · The complex between TCR DMF4 and human Class I MHC HLA-A2 with the bound MART-1(27-35)… · the same entry in another collection · chain A against A, 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
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 3QEQ · PDBe 3QEQ · UniProt P01892 · UniProt P61769
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