Research workbench
Structure of streptococcal pyrogenic exotoxin a
Analyse Structure of streptococcal pyrogenic exotoxin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FNV
- Type
- protein
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exotoxin type a precursor (allele 1)
- UniProt
- P62560
- Ligands
- CD
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Exotoxin type a precursor (allele 1) | protein | 221 | 18% helix, 32% strand | P62560 |
Ligands and binding sites
- CD · Cadmium ion · metal · 16 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.78 | 0.91 | 43 | empty |
| 2 | 158 | 0.74 | 0.92 | 29 | empty |
| 3 | 112 | 0.69 | 0.91 | 25 | empty |
| 4 | 64 | 0.61 | 0.91 | 16 | empty |
| 5 | 198 | 0.56 | 0.79 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–D · 702 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 691 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 686 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 677 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 228 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1FNV · Structure of streptococcal pyrogenic exotoxin a · 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 P62560
- Elsewhere: RCSB PDB 1FNV · PDBe 1FNV · UniProt P62560
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.