Research workbench
Crystal structure of plsy (ygih), an integral membrane glycerol 3- phosphate acyltransferase - the lysphosphatidic acid form
Analyse Crystal structure of plsy (ygih), an integral membrane glycerol 3- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XJ8
- Type
- protein
- Length
- 395 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-3-phosphate acyltransferase
- EC
- 2.3.1.-
- UniProt
- O66905
- Ligands
- NKO, PO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol-3-phosphate acyltransferase (EC 2.3.1.-) | protein | 196 | 74% helix, 0% strand | O66905 |
| B | Glycerol-3-phosphate acyltransferase (EC 2.3.1.-) | protein | 199 | 75% helix, 0% strand | O66905 |
Ligands and binding sites
- NKO · (2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate · ligand · chains B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.80 | 0.90 | 51 | PO4, NKO |
| 2 | 752 | 0.79 | 0.82 | 75 | PO4 |
| 3 | 55 | 0.34 | 0.78 | 17 | empty |
| 4 | 59 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 501 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XJ8 · Crystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- O66905 · AlphaFold monomer V2.0 prediction for glycerol-3-phosphate acyltransferase (O66905) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O66905
- Elsewhere: RCSB PDB 5XJ8 · PDBe 5XJ8 · UniProt O66905
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