MolNFT v1 · #185994 · protein
Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting mage-A10 9-mer peptide
7QPJ · MHC class I antigen: “Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting mage-A10 9-mer peptide”. X-ray diffraction, 10 pockets (best druggability 0.74). MolNFT v1 #185994 on GenesisL1: 3D structure…
- PDB
- 7QPJ
- Type
- protein
- Length
- 823 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Melanoma-associated antigen 10; T-cell…
- UniProt
- Q861F7, P61769, P43363
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | MHC class I antigen | protein | 276 | 28% helix, 39% strand | Q861F7 |
| D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| E | Melanoma-associated antigen 10 | protein | 9 | 0% helix, 0% strand | P43363 |
| A | T-cell receptor alpha chain | protein | 200 | 4% helix, 45% strand | — |
| B | T-cell receptor beta chain | protein | 238 | 8% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.74 | 0.77 | 85 | empty |
| 2 | 559 | 0.66 | 0.77 | 51 | GOL |
| 3 | 211 | 0.60 | 0.81 | 29 | GOL |
| 4 | 92 | 0.50 | 0.82 | 18 | empty |
| 5 | 193 | 0.49 | 0.76 | 26 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2057 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1360 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 812 Ų buried · 14 hydrogen bonds · protein-protein
- C–A · 485 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 340 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7QPJ · Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10… · the same entry in another collection · chain D against D, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P43363 · AlphaFold monomer V2.0 prediction for melanoma-associated antigen 10 (P43363) · a predicted model of the same protein · chain E 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 Q861F7
- Every structure of UniProt P61769
- Every structure of UniProt P43363
- Elsewhere: RCSB PDB 7QPJ · PDBe 7QPJ · UniProt Q861F7 · UniProt P61769 · UniProt P43363
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