Crystal structure analysis of GM2-activator protein complexed with phosphatidylcholine

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).

Ligands and binding sites

• LP3 · (7R)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacosan-1-aminium 4-oxide · ligand · 4 copies · chains A, B, C
• CH5 · 2-(((R)-2,3-dihydroxypropyl)phosphoryloxy)-N,N,N-trimethylethanaminium · ligand · 2 copies · chains B, C
• OLA · Oleic acid · ligand · 2 copies · chains B, C
• MYR · Myristic acid · ligand · 2 copies · chains B, C
• DAO · Lauric acid · ligand · chains B
• CL · Chloride ion · ion · 3 copies · chains A, B, C
• IPA · Isopropyl alcohol · additive · 10 copies · chains A, B, C
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–C · 556 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 549 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

• 2AG2 · Crystal Structure Analysis of GM2-activator protein complexed with Phosphatidylcholine · the same entry in another collection · chain A against A, TM-score 1.00
• P17900 · AlphaFold monomer V2.0 prediction for ganglioside GM2 activator (P17900) · a predicted model of the same protein · chain C 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 P17900
• Elsewhere: RCSB PDB 2AG2 · PDBe 2AG2 · UniProt P17900