Research workbench
Crystal structure of staphylococcal enterotoxin H in complex with human MHC class II
Analyse Crystal structure of staphylococcal enterotoxin H in complex with human MHC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HXY
- Type
- protein
- Length
- 585 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P04229, P0A0M0
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 14% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, dr-1 beta chain | protein | 180 | 18% helix, 47% strand | P04229 |
| C | Hemagglutinin | protein | 13 | 0% helix, 8% strand | — |
| D | Enterotoxin H | protein | 212 | 25% helix, 39% strand | P0A0M0 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.41 | 0.75 | 22 | empty |
| 2 | 153 | 0.39 | 0.73 | 25 | empty |
| 3 | 96 | 0.34 | 0.74 | 16 | empty |
| 4 | 73 | 0.30 | 0.74 | 16 | empty |
| 5 | 66 | 0.28 | 0.73 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2524 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 686 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 668 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 466 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 246 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1HXY · Crystal structure of staphylococcal enterotoxin H in complex with human MHC class II · the same entry in another collection · chain C against C, TM-score 1.00
- P0A0M0 · AlphaFold monomer V2.0 prediction for enterotoxin type H (P0A0M0) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P01903
- Every structure of UniProt P04229
- Every structure of UniProt P0A0M0
- Elsewhere: RCSB PDB 1HXY · PDBe 1HXY · UniProt P01903 · UniProt P04229 · UniProt P0A0M0
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