Research workbench
Structure of the N254Y/H258Y mutant of the phosphatidylinositol- specific phospholipase C from S. aureus bound to DIC4PC
Analyse Structure of the N254Y/H258Y mutant of the phosphatidylinositol- specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I9J
- Type
- protein
- Length
- 302 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-phosphatidylinositol phosphodiesterase
- EC
- 4.6.1.13
- UniProt
- P45723
- Ligands
- XP5
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-phosphatidylinositol phosphodiesterase (EC 4.6.1.13) | protein | 302 | 33% helix, 22% strand | P45723 |
Ligands and binding sites
- XP5 · (4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide · ligand · 3 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.40 | 0.76 | 20 | empty |
Compared structures
- 4I9J · Structure of the N254Y/H258Y mutant of the phosphatidylinositol-specific phospholipase C… · the same entry in another collection · chain A against A, TM-score 1.00
- P45723 · AlphaFold monomer V2.0 prediction for 1-phosphatidylinositol phosphodiesterase (P45723) · 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 P45723
- Elsewhere: RCSB PDB 4I9J · PDBe 4I9J · UniProt P45723
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