Research workbench
Phosphoinositide-specific phospholipase C-DELTA1 from rat complexed with lanthanum
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
- 1DJG
- 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
- LA
- Pockets
- 17 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 30% 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 | 29% helix, 26% strand | P10688 |
| B | Phosphoinositide-specific phospholipase C, isozyme DELTA1 (EC 3.1.4.11) | protein | 561 | 31% helix, 24% strand | P10688 |
Ligands and binding sites
- LA · Lanthanum (III) ion · metal · 8 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
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.67 | 0.88 | 25 | empty |
| 2 | 136 | 0.66 | 0.88 | 25 | empty |
| 3 | 277 | 0.64 | 0.81 | 43 | empty |
| 4 | 248 | 0.62 | 0.81 | 43 | empty |
| 5 | 293 | 0.58 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 635 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1DJG · Phosphoinositide-specific phospholipase C-DELTA1 from rat complexed with lanthanum · 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 1DJG · PDBe 1DJG · UniProt P10688
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