MolNFT v1 · #9694 · protein
Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1I4F · HLA class I histocompatibility antigen, a-2 alpha chain: “Crystal structure of HLA-A*0201/MAGE-A4-peptide complex”. X-ray diffraction, 1 ligand (1PG), 5 pockets (best druggability 0.69). MolNFT v1 #9694 on GenesisL1: 3D structure…
- PDB
- 1I4F
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61769, P43358
- Ligands
- 1PG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 27% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Melanoma-associated antigen 4 | protein | 10 | 0% helix, 0% strand | P43358 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 553 | 0.69 | 0.78 | 53 | 1PG |
| 2 | 87 | 0.42 | 0.79 | 20 | empty |
| 3 | 87 | 0.41 | 0.78 | 20 | empty |
| 4 | 61 | 0.32 | 0.76 | 16 | empty |
| 5 | 53 | 0.27 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1276 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 819 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1I4F · Crystal structure of HLA-A*0201/MAGE-A4-peptide complex · 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
- P43358 · AlphaFold monomer V2.0 prediction for melanoma-associated antigen 4 (P43358) · a predicted model of the same protein · chain C against A, TM-score 0.30
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 P43358
- Elsewhere: RCSB PDB 1I4F · PDBe 1I4F · UniProt P01892 · UniProt P61769 · UniProt P43358
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