Research workbench
Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein
Analyse Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EJM
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.71
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- MHC class I antigen; Beta-2-microglobulin; 9-mer peptide from the HCoV spike protein
- UniProt
- A0A411J078, P61769
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.71 · 3 distinct chains · 19% helix, 41% 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, 48% strand | P61769 |
| C | 9-mer peptide from the HCoV spike protein | protein | 9 | 0% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.70 | 0.78 | 62 | empty |
| 2 | 244 | 0.59 | 0.80 | 33 | empty |
| 3 | 70 | 0.41 | 0.80 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1381 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 948 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EJM · Complex structure of HLA-A*2402 with the peptide from HCOV(COV-229E) 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 7EJM · PDBe 7EJM · UniProt A0A411J078 · UniProt P61769
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