Research workbench
Crystal structure of HLA-A*11:01 in complex with nsasfstfk, an 9-mer epitope from SARS-cov-2 spike (S370-378)
Analyse Crystal structure of HLA-A*11:01 in complex with nsasfstfk, an 9-mer epitope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M8T
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a alpha chain; Beta-2-microglobulin; Spike…
- UniProt
- U5YJK1, P61769, P0DTC2
- Ligands
- NA, CA, SO4, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a alpha chain | protein | 276 | 26% helix, 39% strand | U5YJK1 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Spike protein S1 peptide | protein | 9 | 0% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 578 | 0.66 | 0.77 | 62 | CL |
| 2 | 203 | 0.51 | 0.77 | 33 | SO4 |
| 3 | 56 | 0.41 | 0.82 | 21 | empty |
| 4 | 72 | 0.34 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1386 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 880 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7M8T · Crystal Structure of HLA-A*11:01 in complex with NSASFSTFK, an 9-mer epitope from… · 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 U5YJK1
- Every structure of UniProt P61769
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7M8T · PDBe 7M8T · UniProt U5YJK1 · UniProt P61769 · UniProt P0DTC2
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