MolNFT v1 · #180491 · protein
Crystal structure of human 21LT2-2 TCR bound to HLA-A*03:01 in complex with a mutant PIK3CA peptide
7L1D · HLA class I histocompatibility antigen, a alpha chain: “Crystal structure of human 21LT2-2 TCR bound to HLA-A*03:01 in complex with a mutant PIK3CA peptide”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #180491…
- PDB
- 7L1D
- Type
- protein
- Length
- 816 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a alpha chain; Beta-2-microglobulin; Mutant…
- UniProt
- P04439, P61769, P42336
- Pockets
- 8 · best druggability 0.71
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 alpha chain | protein | 274 | 26% helix, 39% strand | P04439 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| C | Mutant PIK3CA peptide | protein | 9 | 0% helix, 0% strand | P42336 |
| D | T cell receptor, alpha chain | protein | 187 | 3% helix, 42% strand | — |
| E | T cell receptor, beta chain | protein | 247 | 6% helix, 51% strand | — |
Ligands and binding sites
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 | 670 | 0.71 | 0.78 | 61 | empty |
| 2 | 739 | 0.69 | 0.77 | 72 | GOL |
| 3 | 172 | 0.47 | 0.76 | 18 | empty |
| 4 | 94 | 0.47 | 0.81 | 19 | empty |
| 5 | 105 | 0.45 | 0.79 | 20 | empty |
Interfaces
4 interfaces between chains.
- D–E · 2045 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1347 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 909 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 292 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7L1D · Crystal structure of human 21LT2-2 TCR bound to HLA-A*03:01 in complex with a mutant… · the same entry in another collection · chain E against E, TM-score 1.00
- P04439 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, a alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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
- P42336 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate 3-kinase… · a predicted model of the same protein · chain C against A, TM-score 0.49
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 P04439
- Every structure of UniProt P61769
- Every structure of UniProt P42336
- Elsewhere: RCSB PDB 7L1D · PDBe 7L1D · UniProt P04439 · UniProt P61769 · UniProt P42336
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