Research workbench
SARS-cov-2 spike-derived peptide S269-277 (ylqprtfll) presented by HLA-A*02:01
Analyse SARS-cov-2 spike-derived peptide S269-277 (ylqprtfll) presented by HLA-A*02:01 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RTD
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I antigen; Beta-2-microglobulin; Spike protein S1
- UniProt
- Q53Z42, P61769, P0DTC2
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I antigen | protein | 274 | 27% helix, 41% strand | Q53Z42 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Spike protein S1 | protein | 9 | 0% helix, 0% strand | P0DTC2 |
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 | 626 | 0.67 | 0.76 | 58 | empty |
| 2 | 85 | 0.42 | 0.79 | 18 | empty |
| 3 | 66 | 0.31 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1345 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 929 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7RTD · SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01 · 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 0.98
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 Q53Z42
- Every structure of UniProt P61769
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7RTD · PDBe 7RTD · UniProt Q53Z42 · UniProt P61769 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.