Research workbench
Phosphoinositide-specific phospholipase C-DELTA1 from rat complexed with inositol-4,5-bisphosphate
Analyse Phosphoinositide-specific phospholipase C-DELTA1 from rat complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DJZ
- Type
- protein
- Length
- 1,074 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoinositide-specific phospholipase C, isozyme DELTA1
- EC
- 3.1.4.11
- UniProt
- P10688
- Ligands
- IP2, CA
- Pockets
- 19 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoinositide-specific phospholipase C, isozyme DELTA1 (EC 3.1.4.11) | protein | 513 | 30% helix, 26% strand | P10688 |
| B | Phosphoinositide-specific phospholipase C, isozyme DELTA1 (EC 3.1.4.11) | protein | 561 | 32% helix, 24% strand | P10688 |
Ligands and binding sites
- IP2 · D-myo-inositol-4,5-bisphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.69 | 0.89 | 23 | empty |
| 2 | 161 | 0.68 | 0.88 | 24 | empty |
| 3 | 301 | 0.65 | 0.81 | 44 | empty |
| 4 | 276 | 0.63 | 0.81 | 45 | empty |
| 5 | 295 | 0.59 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1DJZ · Phosphoinositide-specific phospholipase C-DELTA1 from rat complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P10688 · AlphaFold monomer V2.0 prediction for 1-phosphatidylinositol 4,5-bisphosphate… · 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 P10688
- Elsewhere: RCSB PDB 1DJZ · PDBe 1DJZ · UniProt P10688
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