Research workbench
Crystal structure of the Y246S/Y247S/Y248S/Y251S mutant of phosphatidylinositol-specific phospholipase C from bacillus thuringiensis
Analyse Crystal structure of the Y246S/Y247S/Y248S/Y251S mutant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EA3
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-phosphatidylinositol phosphodiesterase
- EC
- 4.6.1.13
- UniProt
- P08954
- Ligands
- MN
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-phosphatidylinositol phosphodiesterase (EC 4.6.1.13) | protein | 296 | 33% helix, 21% strand | P08954 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 5 copies · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.47 | 0.77 | 27 | MN |
| 2 | 146 | 0.47 | 0.77 | 30 | MN |
| 3 | 123 | 0.37 | 0.73 | 24 | empty |
| 4 | 54 | 0.28 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 302 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3EA3 · Crystal Structure of the Y246S/Y247S/Y248S/Y251S Mutant of Phosphatidylinositol-Specific… · the same entry in another collection · chain A against A, TM-score 1.00
- P08954 · AlphaFold monomer V2.0 prediction for 1-phosphatidylinositol phosphodiesterase (P08954) · 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 P08954
- Elsewhere: RCSB PDB 3EA3 · PDBe 3EA3 · UniProt P08954
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.