Research workbench
Complex structure of HLA-A*2402 with the peptide from HCOV(COV-2) spike protein
Analyse Complex structure of HLA-A*2402 with the peptide from HCOV(COV-2) spike protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EJL
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; 9-mer peptide from the hcov spike protein
- UniProt
- A0A411J078, P61769
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 274 | 27% helix, 40% strand | A0A411J078 |
| B | Beta-2-microglobulin | protein | 103 | 0% helix, 50% strand | P61769 |
| C | 9-mer peptide from the hcov spike protein | protein | 9 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.69 | 0.78 | 59 | empty |
| 2 | 227 | 0.58 | 0.80 | 36 | empty |
| 3 | 54 | 0.45 | 0.84 | 16 | empty |
| 4 | 66 | 0.39 | 0.79 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1404 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 993 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EJL · Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein · 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 0.96
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 7EJL · PDBe 7EJL · UniProt A0A411J078 · UniProt P61769
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