MolNFT v1 · #19137 · protein
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta complex with samarium (III) chloride
1QAT · Phospholipase C delta-1: “1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta complex with samarium (III) chloride”. X-ray diffraction, 1 ligand (SM), 15 pockets (best druggability 0.67). MolNFT v1 #19137 on GenesisL1…
- PDB
- 1QAT
- Type
- protein
- Length
- 1,016 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase C delta-1
- EC
- 3.1.4.11
- UniProt
- P10688
- Ligands
- SM
- Pockets
- 15 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase C delta-1 (EC 3.1.4.11) | protein | 509 | 28% helix, 25% strand | P10688 |
| B | Phospholipase C delta-1 (EC 3.1.4.11) | protein | 507 | 29% helix, 25% strand | P10688 |
Ligands and binding sites
- SM · Samarium (III) ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.67 | 0.86 | 25 | empty |
| 2 | 155 | 0.66 | 0.86 | 28 | empty |
| 3 | 214 | 0.58 | 0.80 | 47 | empty |
| 4 | 312 | 0.58 | 0.77 | 33 | empty |
| 5 | 217 | 0.52 | 0.77 | 41 | SM |
Interfaces
1 interface between chains.
- A–B · 652 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1QAT · 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta complex with samarium… · the same entry in another collection · chain B against B, TM-score 1.00
- P10688 · AlphaFold monomer V2.0 prediction for 1-phosphatidylinositol 4,5-bisphosphate… · a predicted model of the same protein · chain B 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 1QAT · PDBe 1QAT · UniProt P10688
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