Research workbench
Crystal structure of the superantigen smez-2 (zinc bound) from streptococcus pyogenes
Analyse Crystal structure of the superantigen smez-2 (zinc bound) from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EU3
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superantigen smez-2
- UniProt
- Q9RQQ5
- Ligands
- ZN, K, PO4
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superantigen smez-2 | protein | 210 | 20% helix, 41% strand | Q9RQQ5 |
| B | Superantigen smez-2 | protein | 208 | 18% helix, 41% strand | Q9RQQ5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains 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 | 162 | 0.55 | 0.81 | 23 | empty |
| 2 | 196 | 0.48 | 0.76 | 34 | empty |
| 3 | 56 | 0.33 | 0.78 | 19 | empty |
| 4 | 58 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1EU3 · Crystal structure of the superantigen smez-2 (zinc bound) from streptococcus pyogenes · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9RQQ5
- Elsewhere: RCSB PDB 1EU3 · PDBe 1EU3 · UniProt Q9RQQ5
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