Research workbench
Crystal structure of a pentafluoro-phe incorporated phosphatidylinositol-specific phospholipase C (H258X)FROM staphylococcus aureus
Analyse Crystal structure of a pentafluoro-phe incorporated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RV3
- 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
- INS
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-phosphatidylinositol phosphodiesterase (EC 4.6.1.13) | protein | 302 | 34% helix, 22% strand | P45723 |
Ligands and binding sites
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.47 | 0.78 | 24 | INS |
| 2 | 54 | 0.30 | 0.76 | 14 | empty |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4RV3 · Crystal structure of a pentafluoro-Phe incorporated Phosphatidylinositol-specific… · 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 4RV3 · PDBe 4RV3 · UniProt P45723
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