Research workbench
Poor binding of a her-2/NEU epitope (GP2) to HLA-A2.1 is due to a lack of interactions in the center of the peptide
Analyse Poor binding of a her-2/NEU epitope (GP2) to HLA-A2.1 is due to a lack of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QR1
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-A2.1 heavy chain; Beta-2 microglobulin; GP2 peptide
- UniProt
- P01892, P61769, P04626
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA-A2.1 heavy chain | protein | 275 | 27% helix, 39% strand | P01892 |
| B, E | Beta-2 microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | GP2 peptide | protein | 9 | 0% helix, 0% strand | P04626 |
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 | 610 | 0.69 | 0.78 | 62 | empty |
| 2 | 598 | 0.68 | 0.77 | 58 | empty |
| 3 | 143 | 0.49 | 0.79 | 24 | empty |
| 4 | 159 | 0.49 | 0.78 | 25 | empty |
| 5 | 79 | 0.43 | 0.80 | 21 | empty |
Interfaces
4 interfaces between chains.
- D–E · 1406 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1402 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 835 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 820 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1QR1 · Poor binding of a her-2/NEU epitope (GP2) to HLA-A2.1 is due to a lack of interactions in… · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P04626 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-2 (P04626) · a predicted model of the same protein · chain C 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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt P04626
- Elsewhere: RCSB PDB 1QR1 · PDBe 1QR1 · UniProt P01892 · UniProt P61769 · UniProt P04626
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