Research workbench
SARS-cov-2 ylq peptide binds to HLA-A2
Analyse SARS-cov-2 ylq peptide binds to HLA-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N1A
- Type
- protein
- Length
- 766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen, a-2 alpha chain; Beta-2-microglobulin; Spike protein S1
- UniProt
- A0A5B8RNS7, P61769, P0DTC2
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen, a-2 alpha chain | protein | 275 | 28% helix, 40% strand | A0A5B8RNS7 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Spike protein S1 | protein | 9 | 0% helix, 0% strand | P0DTC2 |
| D | MHC class I antigen, a-2 alpha chain | protein | 273 | 27% helix, 40% strand | A0A5B8RNS7 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.77 | 0.81 | 88 | empty |
| 2 | 346 | 0.66 | 0.80 | 49 | PG4 |
| 3 | 88 | 0.48 | 0.82 | 18 | empty |
| 4 | 101 | 0.46 | 0.79 | 18 | empty |
| 5 | 96 | 0.45 | 0.80 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1401 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1318 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 930 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 924 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 752 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 A0A5B8RNS7
- Every structure of UniProt P61769
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7N1A · PDBe 7N1A · UniProt A0A5B8RNS7 · UniProt P61769 · UniProt P0DTC2
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