Research workbench
Integrated illustration of a valid epitope based on the sla class I structure and tetramer technique could carry forward the development of molecular vaccine in swine species
Analyse Integrated illustration of a valid epitope based on the sla class I structure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YLX
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Prrsv-NSP9-TMP9 peptide
- UniProt
- H6TIB1, Q07717, I6YDJ5
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 275 | 29% helix, 39% strand | H6TIB1 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | Q07717 |
| C | Prrsv-NSP9-TMP9 peptide | protein | 9 | 0% helix, 0% strand | I6YDJ5 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.69 | 0.79 | 50 | empty |
| 2 | 135 | 0.46 | 0.77 | 17 | empty |
| 3 | 72 | 0.41 | 0.80 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1397 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 851 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5YLX · Integrated illustration of a valid epitope based on the SLA class I structure and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07717 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q07717) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 H6TIB1
- Every structure of UniProt Q07717
- Every structure of UniProt I6YDJ5
- Elsewhere: RCSB PDB 5YLX · PDBe 5YLX · UniProt H6TIB1 · UniProt Q07717 · UniProt I6YDJ5
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