MolNFT v1 · #179215 · protein
Crystal structure of HLA A*2402 in complex with yfspirvtf, an 9-mer influenza epitope
7JYV · MHC class I antigen: “Crystal structure of HLA A*2402 in complex with yfspirvtf, an 9-mer influenza epitope”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.67). MolNFT v1 #179215 on GenesisL1: 3D structure…
- PDB
- 7JYV
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Np peptide from influenza, yfspirvtf
- UniProt
- A0A411J078, P61769
- Ligands
- MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 26% helix, 40% strand | A0A411J078 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Np peptide from influenza, yfspirvtf | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.67 | 0.77 | 58 | empty |
| 2 | 70 | 0.35 | 0.76 | 15 | empty |
| 3 | 69 | 0.33 | 0.75 | 16 | empty |
| 4 | 74 | 0.31 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1448 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 978 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7JYV · Crystal Structure of HLA A*2402 in complex with YFSPIRVTF, an 9-mer influenza epitope · 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
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 7JYV · PDBe 7JYV · UniProt A0A411J078 · UniProt P61769
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