Research workbench
The structure of the MHC class I molecule of bony fishes provides insights into the conserved nature of the antigen-presenting system
Analyse The structure of the MHC class I molecule of bony fishes provides insights into… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y91
- Type
- protein
- Length
- 379 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Peptide phe-ala-asn-phe-cys-leu-met-met-ile
- UniProt
- Q65XY8, Q65XZ7
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 273 | 27% helix, 40% strand | Q65XY8 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 54% strand | Q65XZ7 |
| C | Peptide phe-ala-asn-phe-cys-leu-met-met-ile | protein | 9 | 0% helix, 0% strand | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.65 | 0.77 | 49 | empty |
| 2 | 120 | 0.48 | 0.79 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1835 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 876 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5Y91 · The structure of the MHC class I molecule of bony fishes provides insights into the… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q65XY8
- Every structure of UniProt Q65XZ7
- Elsewhere: RCSB PDB 5Y91 · PDBe 5Y91 · UniProt Q65XY8 · UniProt Q65XZ7
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