Research workbench
Crystal structure of piratoxin I (prtx-I) complexed to aristolochic acid
Analyse Crystal structure of piratoxin I (prtx-I) complexed to aristolochic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YZ7
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic phospholipase A2 homolog piratoxin-1
- UniProt
- P58399
- Ligands
- 9AR, SO4
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Basic phospholipase A2 homolog piratoxin-1 | protein | 121 | 49% helix, 11% strand | P58399 |
Ligands and binding sites
- 9AR · 9-hydroxy aristolochic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.76 | 0.80 | 69 | PE4 |
Interfaces
1 interface between chains.
- A–B · 337 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4YZ7 · Crystal structure of Piratoxin I (PrTX-I) complexed to aristolochic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P58399 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog piratoxin-1 (P58399) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P58399
- Elsewhere: RCSB PDB 4YZ7 · PDBe 4YZ7 · UniProt P58399
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