Research workbench
The high resolution crystal structure of HLA-A1 complexed with the mage-A1 peptide
Analyse The high resolution crystal structure of HLA-A1 complexed with the mage-A1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BO8
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-1 alpha chain; Beta-2-microglobulin; Nonameric…
- UniProt
- P30443, P61769, P43355
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-1 alpha chain | protein | 274 | 28% helix, 39% strand | P30443 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Nonameric peptide from melanoma-associated antigen 1 | protein | 9 | 0% helix, 0% strand | P43355 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.67 | 0.77 | 55 | GOL |
| 2 | 123 | 0.47 | 0.79 | 22 | empty |
| 3 | 58 | 0.31 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1357 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 865 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3BO8 · The High Resolution Crystal Structure of HLA-A1 Complexed with the MAGE-A1 Peptide · 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 0.98
- P43355 · AlphaFold monomer V2.0 prediction for melanoma-associated antigen 1 (P43355) · a predicted model of the same protein · chain C against A, TM-score 0.43
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 P30443
- Every structure of UniProt P61769
- Every structure of UniProt P43355
- Elsewhere: RCSB PDB 3BO8 · PDBe 3BO8 · UniProt P30443 · UniProt P61769 · UniProt P43355
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