Research workbench
Crystal structure of the zymogen form of streptococcal pyrogenic exotoxin B active site (C47S) mutant
Analyse Crystal structure of the zymogen form of streptococcal pyrogenic exotoxin B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DKI
- Type
- protein
- Length
- 1,296 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrogenic exotoxin B zymogen
- UniProt
- P0C0J0
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrogenic exotoxin B zymogen | protein | 303 | 27% helix, 22% strand | P0C0J0 |
| B | Pyrogenic exotoxin B zymogen | protein | 320 | 26% helix, 21% strand | P0C0J0 |
| C | Pyrogenic exotoxin B zymogen | protein | 339 | 27% helix, 21% strand | P0C0J0 |
| D | Pyrogenic exotoxin B zymogen | protein | 334 | 28% helix, 20% strand | P0C0J0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.78 | 0.87 | 69 | SO4 |
| 2 | 432 | 0.78 | 0.87 | 75 | SO4 |
| 3 | 93 | 0.54 | 0.85 | 16 | empty |
| 4 | 52 | 0.45 | 0.84 | 16 | empty |
| 5 | 111 | 0.42 | 0.77 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 868 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 777 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 298 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 275 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 264 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1DKI · Crystal structure of the zymogen form of streptococcal pyrogenic exotoxin B active site… · the same entry in another collection · chain D against D, TM-score 1.00
- P0C0J0 · AlphaFold monomer V2.0 prediction for streptopain (P0C0J0) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P0C0J0
- Elsewhere: RCSB PDB 1DKI · PDBe 1DKI · UniProt P0C0J0
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