MolNFT v1 · #179217 · protein
Crystal structure of HLA A*2402 in complex with tyqwiirnwet, an 11-mer epitope from influenza
7JYX · MHC class I antigen: “Crystal structure of HLA A*2402 in complex with tyqwiirnwet, an 11-mer epitope from influenza”. X-ray diffraction, 7 pockets (best druggability 0.68). MolNFT v1 #179217 on GenesisL1: 3D structure, binding sites…
- PDB
- 7JYX
- Type
- protein
- Length
- 766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; PB2 peptide from influenza, tyqwiirnwet
- UniProt
- A0A411J078, P61769
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 272 | 25% helix, 38% strand | A0A411J078 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C, F | PB2 peptide from influenza, tyqwiirnwet | protein | 11 | 0% helix, 0% strand | — |
| D | MHC class I antigen | protein | 274 | 26% helix, 39% strand | A0A411J078 |
| E | Beta-2-microglobulin | protein | 100 | 0% helix, 47% strand | P61769 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.68 | 0.78 | 54 | empty |
| 2 | 483 | 0.66 | 0.78 | 53 | empty |
| 3 | 447 | 0.66 | 0.79 | 62 | empty |
| 4 | 184 | 0.54 | 0.79 | 30 | empty |
| 5 | 108 | 0.48 | 0.80 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1391 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1387 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1132 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1103 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 208 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7JYX · Crystal Structure of HLA A*2402 in complex with TYQWIIRNWET, an 11-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 7JYX · PDBe 7JYX · UniProt A0A411J078 · UniProt P61769
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