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Human GM2 activator protein paf complex

Analyse Human GM2 activator protein paf complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1TJJ
Type: protein
Length: 491 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ganglioside GM2 activator
UniProt: P17900
Ligands: PFS, LPE, DAO, CL
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ganglioside GM2 activator	protein	164	7% helix, 51% strand	P17900
C	Ganglioside GM2 activator	protein	163	7% helix, 49% strand	P17900

Ligands and binding sites

PFS · (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate · ligand · 3 copies · chains A, B, C
LPE · 1-O-octadecyl-sn-glycero-3-phosphocholine · ligand · 3 copies · chains A, B, C
DAO · Lauric acid · ligand · chains B
CL · Chloride ion · ion · 3 copies · chains A, B, C
ACT · Acetate ion · additive · 5 copies · chains A, B, C
IPA · Isopropyl alcohol · additive · 5 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1147	0.79	0.80	62	ACT, PFS, LPE, DAO
2	1157	0.78	0.79	66	ACT, PFS, LPE, IPA
3	1195	0.78	0.80	70	ACT, PFS, LPE, IPA

Interfaces

2 interfaces between chains.

A–C · 561 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 551 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

1TJJ · Human GM2 Activator Protein PAF complex · 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 0.95

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 1TJJ · PDBe 1TJJ · UniProt P17900

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