MolNFT v1 · #179216 · protein
Crystal structure of HLA A*2402 in complex with tyqwiirnw, an 9-mer influenza epitope
7JYW · MHC class I antigen: “Crystal structure of HLA A*2402 in complex with tyqwiirnw, an 9-mer influenza epitope”. X-ray diffraction, 3 ligands (NA, CA, NI), 4 pockets (best druggability 0.69). MolNFT v1 #179216 on GenesisL1: 3D…
- PDB
- 7JYW
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; PB2 peptide from influenza, tyqwiirnw
- UniProt
- A0A411J078, P61769
- Ligands
- NA, CA, NI
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 275 | 26% helix, 37% strand | A0A411J078 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C | PB2 peptide from influenza, tyqwiirnw | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A, B
- NI · Nickel (II) ion · metal · chains B
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 | 666 | 0.69 | 0.77 | 59 | empty |
| 2 | 148 | 0.48 | 0.78 | 22 | CA |
| 3 | 93 | 0.44 | 0.79 | 14 | NA |
| 4 | 64 | 0.30 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1335 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1027 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7JYW · Crystal Structure of HLA A*2402 in complex with TYQWIIRNW, 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 0.97
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 7JYW · PDBe 7JYW · UniProt A0A411J078 · UniProt P61769
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