Research workbench
Crystal structure of HLA-B*07:02 in complex with an ny-eso-1 peptide
Analyse Crystal structure of HLA-B*07:02 in complex with an ny-eso-1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AT5
- Type
- protein
- Length
- 387 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-7 alpha chain; Beta-2-microglobulin…
- UniProt
- P01889, P61769, P78358
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 275 | 27% helix, 40% strand | P01889 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | CANCER/TESTIS antigen 1 peptide | protein | 13 | 0% helix, 0% strand | P78358 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.69 | 0.78 | 51 | empty |
| 2 | 159 | 0.48 | 0.77 | 27 | empty |
| 3 | 74 | 0.46 | 0.83 | 22 | empty |
| 4 | 60 | 0.37 | 0.79 | 16 | empty |
| 5 | 52 | 0.28 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1338 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 822 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6AT5 · Crystal structure of HLA-B*07:02 in complex with an NY-ESO-1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P01889 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, B alpha… · a predicted model of the same protein · 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 0.98
- P78358 · AlphaFold monomer V2.0 prediction for CANCER/TESTIS antigen 1 (P78358) · a predicted model of the same protein · chain C against A, TM-score 0.23
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 P01889
- Every structure of UniProt P61769
- Every structure of UniProt P78358
- Elsewhere: RCSB PDB 6AT5 · PDBe 6AT5 · UniProt P01889 · UniProt P61769 · UniProt P78358
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