Research workbench
Crystal structure of the streptococcal pyrogenic exotoxin B (speb)- inhibitor complex
Analyse Crystal structure of the streptococcal pyrogenic exotoxin B (speb)- inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PVJ
- Type
- protein
- Length
- 1,356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrogenic exotoxin B
- EC
- 3.4.22.10
- UniProt
- P0C0J0
- Ligands
- ZFB
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyrogenic exotoxin B (EC 3.4.22.10) | protein | 339 | 29% helix, 19% strand | P0C0J0 |
Ligands and binding sites
- ZFB · (3R)-3-{[(benzyloxy)carbonyl]amino}-2-oxo-4-phenylbutane-1-diazonium · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.80 | 0.84 | 108 | ZFB |
| 2 | 730 | 0.80 | 0.84 | 106 | ZFB |
| 3 | 245 | 0.52 | 0.76 | 38 | empty |
| 4 | 54 | 0.44 | 0.84 | 19 | empty |
| 5 | 53 | 0.39 | 0.82 | 11 | empty |
Interfaces
5 interfaces between chains.
- C–D · 869 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 862 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 278 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 277 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 198 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1PVJ · Crystal structure of the Streptococcal pyrogenic exotoxin B (SpeB)- inhibitor complex · the same entry in another collection · chain A against A, TM-score 1.00
- P0C0J0 · AlphaFold monomer V2.0 prediction for streptopain (P0C0J0) · a predicted model of the same protein · chain A 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 1PVJ · PDBe 1PVJ · UniProt P0C0J0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.