MolNFT v1 · #187305 · protein
Crystal structure of HLA A*1101 in complex with salewiknk, an 9-mer epitope from influenza B
7S8R · HLA class I histocompatibility antigen, a alpha chain: “Crystal structure of HLA A*1101 in complex with salewiknk, an 9-mer epitope from influenza B”. X-ray diffraction, 2 ligands (MG, SO4), 9 pockets (best druggability 0.74).…
- PDB
- 7S8R
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a alpha chain; Beta-2-microglobulin; Matrix…
- UniProt
- U5YJK1, P61769, P13879
- Ligands
- MG, SO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a alpha chain | protein | 275 | 23% helix, 40% strand | U5YJK1 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C, F | Matrix protein 1 peptide salewiknk | protein | 9 | 0% helix, 0% strand | P13879 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.74 | 0.77 | 66 | empty |
| 2 | 1106 | 0.71 | 0.75 | 88 | MG, SO4 |
| 3 | 750 | 0.70 | 0.77 | 60 | MG |
| 4 | 627 | 0.68 | 0.77 | 57 | MG |
| 5 | 168 | 0.44 | 0.75 | 24 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1424 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1393 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 952 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 908 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 400 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7S8R · Crystal Structure of HLA A*1101 in complex with SALEWIKNK, an 9-mer epitope from… · the same entry in another collection · chain E against E, 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 U5YJK1
- Every structure of UniProt P61769
- Every structure of UniProt P13879
- Elsewhere: RCSB PDB 7S8R · PDBe 7S8R · UniProt U5YJK1 · UniProt P61769 · UniProt P13879
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