Research workbench
Crystal structure of HLA-A*2402 in complex with iyfspirvtf, an 10-mer epitope from influenza B virus
Analyse Crystal structure of HLA-A*2402 in complex with iyfspirvtf, an 10-mer epitope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JYU
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Np-164-173 peptide from influenza B, iyfspirvtf
- UniProt
- A0A411J078, P61769
- Ligands
- MG
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 275 | 27% helix, 41% strand | A0A411J078 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | Np-164-173 peptide from influenza B, iyfspirvtf | protein | 10 | 0% helix, 0% strand | — |
| D | MHC class I antigen | protein | 274 | 26% helix, 39% strand | A0A411J078 |
| E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.74 | 0.78 | 84 | empty |
| 2 | 763 | 0.68 | 0.75 | 65 | empty |
| 3 | 684 | 0.68 | 0.76 | 63 | empty |
| 4 | 55 | 0.43 | 0.83 | 16 | empty |
| 5 | 132 | 0.43 | 0.76 | 22 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1415 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1236 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 968 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 964 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 158 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7JYU · Crystal Structure of HLA-A*2402 in complex with IYFSPIRVTF, an 10-mer epitope from… · 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
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 A0A411J078
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7JYU · PDBe 7JYU · UniProt A0A411J078 · UniProt P61769
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