Research workbench
SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented by HLA-A*29:02
Analyse SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented by HLA-A*29:02 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TLT
- Type
- protein
- Length
- 767 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, A alpha chain; Beta-2-microglobulin; Spike…
- UniProt
- B0UXQ0, P61769, P0DTC2
- Ligands
- MG, NA, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.3 · 4 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class I histocompatibility antigen, A alpha chain | protein | 275 | 26% helix, 40% strand | B0UXQ0 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| E, F | Spike protein S1 peptide | protein | 9 | 0% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, E, B
- NA · Sodium ion · metal · 2 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.73 | 0.78 | 74 | empty |
| 2 | 958 | 0.72 | 0.76 | 77 | NA |
| 3 | 178 | 0.48 | 0.76 | 30 | empty |
| 4 | 123 | 0.41 | 0.76 | 19 | SO4 |
| 5 | 109 | 0.39 | 0.76 | 24 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1367 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1335 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 969 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 963 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 802 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 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 B0UXQ0
- Every structure of UniProt P61769
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7TLT · PDBe 7TLT · UniProt B0UXQ0 · UniProt P61769 · UniProt P0DTC2
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