MolNFT v1 · #62251 · protein
Crystal structure of the myo-inositol bound Y247S/Y251S mutant of phosphatidylinositol-specific phospholipase C from bacillus thuringiensis
3EA2 · 1-phosphatidylinositol phosphodiesterase: “Crystal structure of the myo-inositol bound Y247S/Y251S mutant of phosphatidylinositol-specific phospholipase…”. X-ray diffraction, 2 ligands (INS, ZN), 3 pockets (best druggability 0.46).…
- PDB
- 3EA2
- 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
- INS, ZN
- Pockets
- 3 · best druggability 0.46
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
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.46 | 0.77 | 25 | INS |
| 2 | 132 | 0.45 | 0.77 | 23 | INS |
| 3 | 145 | 0.38 | 0.73 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 45 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3EA2 · Crystal Structure of the Myo-inositol bound Y247S/Y251S Mutant of… · 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 3EA2 · PDBe 3EA2 · UniProt P08954
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