MolNFT v1 · #37688 · protein
Crystal structure of staphylococcal enterotoxin I (sei) in complex with a human MHC class II molecule
2G9H · HLA class II histocompatibility antigen, dr alpha chain: “Crystal structure of staphylococcal enterotoxin I (sei) in complex with a human MHC class II molecule”. X-ray diffraction, 2 ligands (ZN, SO4), 5 pockets (best druggability…
- PDB
- 2G9H
- Type
- protein
- Length
- 594 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, P04664, O85383
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 14% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 190 | 18% helix, 47% strand | P04229 |
| C | Hemagglutinin | protein | 13 | 0% helix, 8% strand | P04664 |
| D | Extracellular enterotoxin type I | protein | 213 | 20% helix, 37% strand | O85383 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, D
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.47 | 0.76 | 30 | empty |
| 2 | 194 | 0.45 | 0.74 | 24 | EPE |
| 3 | 145 | 0.44 | 0.76 | 26 | SO4 |
| 4 | 141 | 0.43 | 0.75 | 23 | empty |
| 5 | 89 | 0.31 | 0.72 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2472 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 688 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 648 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 482 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 151 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2G9H · Crystal Structure of Staphylococcal Enterotoxin I (SEI) in Complex with a Human MHC class… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.96
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 P04664
- Every structure of UniProt O85383
- Elsewhere: RCSB PDB 2G9H · PDBe 2G9H · UniProt P01903 · UniProt P04229 · UniProt P04664 · UniProt O85383
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.