Research workbench
Crystal Structure Analysis of NY-ESO-1 epitope analogue, SLLMWITQA, in complex with HLA-A2
Analyse Crystal Structure Analysis of NY-ESO-1 epitope analogue, SLLMWITQA, in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S9X
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, A-2 alpha chain; Beta-2-microglobulin; NY-ESO-1…
- UniProt
- P01892, P61769
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.5 · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, A-2 alpha chain | protein | 274 | 28% helix, 41% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | NY-ESO-1 peptide analogue S9A | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.67 | 0.77 | 55 | empty |
| 2 | 154 | 0.50 | 0.78 | 29 | SO4 |
| 3 | 62 | 0.36 | 0.78 | 15 | empty |
| 4 | 63 | 0.35 | 0.78 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1390 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 870 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1S9X · Crystal structure analysis of ny-eso-1 epitope analogue, sllmwitqa, in complex with HLA-A2 · 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 0.99
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 1S9X · PDBe 1S9X · UniProt P01892 · UniProt P61769
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