Research workbench
Crystal structure of plant phospholipase D alpha complex with phosphatidic acid
Analyse Crystal structure of plant phospholipase D alpha complex with phosphatidic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KZ8
- Type
- protein
- Length
- 1,568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase D alpha 1
- EC
- 3.1.4.4
- UniProt
- Q38882
- Ligands
- PA8, CA
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase D alpha 1 (EC 3.1.4.4) | protein | 784 | 24% helix, 25% strand | Q38882 |
Ligands and binding sites
- PA8 · 1,2-dioctanoyl-sn-glycero-3-phosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.78 | 0.82 | 99 | empty |
| 2 | 552 | 0.77 | 0.84 | 62 | empty |
| 3 | 842 | 0.74 | 0.78 | 78 | PA8 |
| 4 | 611 | 0.71 | 0.79 | 51 | PA8 |
| 5 | 839 | 0.68 | 0.75 | 75 | empty |
Interfaces
1 interface between chains.
- A–B · 145 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KZ8 · Crystal structure of plant Phospholipase D alpha complex with phosphatidic acid · the same entry in another collection · chain A against A, TM-score 1.00
- Q38882 · AlphaFold monomer V2.0 prediction for phospholipase D alpha 1 (Q38882) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q38882
- Elsewhere: RCSB PDB 6KZ8 · PDBe 6KZ8 · UniProt Q38882
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