Research workbench
Crystal structure of plsy (ygih), an integral membrane glycerol 3- phosphate acyltransferase - the glycerol 3-phosphate 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
- 5XJ6
- Type
- protein
- Length
- 200 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-3-phosphate acyltransferase
- EC
- 2.3.1.-
- UniProt
- O66905
- Ligands
- G3P, PO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol-3-phosphate acyltransferase (EC 2.3.1.-) | protein | 200 | 75% helix, 0% strand | O66905 |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.78 | 0.86 | 55 | G3P, OLC, PO4 |
| 2 | 71 | 0.36 | 0.78 | 16 | empty |
Compared structures
- 5XJ6 · 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 A 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 5XJ6 · PDBe 5XJ6 · UniProt O66905
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