Research workbench
X-ray structure of the R70D pi-plc enzyme: insight into the role of calcium and surrounding amino acids on active site geometry and catalysis.
Analyse X-ray structure of the R70D pi-plc enzyme: insight into the role of calcium and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T6M
- 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
- CA
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-phosphatidylinositol phosphodiesterase (EC 4.6.1.13) | protein | 296 | 32% helix, 21% strand | P08954 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.62 | 0.81 | 34 | CA |
| 2 | 196 | 0.53 | 0.78 | 34 | CA |
| 3 | 89 | 0.42 | 0.79 | 17 | empty |
| 4 | 131 | 0.39 | 0.74 | 21 | empty |
| 5 | 72 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 423 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1T6M · X-ray Structure of the R70D PI-PLC enzyme: Insight into the role of calcium and… · 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 1T6M · PDBe 1T6M · UniProt P08954
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