MolNFT v1 · #18597 · protein

GM2-activator protein crystal structure

1PU5 · Ganglioside GM2 activator: “GM2-activator protein crystal structure”. X-ray diffraction, 3 pockets (best druggability 0.81). MolNFT v1 #18597 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PU5
Type: protein
Length: 489 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ganglioside GM2 activator
UniProt: P17900
Pockets: 3 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ganglioside GM2 activator	protein	164	7% helix, 52% strand	P17900
C	Ganglioside GM2 activator	protein	161	5% helix, 50% strand	P17900

Ligands and binding sites

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	979	0.81	0.82	59	empty
2	1190	0.79	0.80	64	empty
3	1191	0.78	0.79	69	empty

Interfaces

2 interfaces between chains.

A–C · 563 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 554 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

1PU5 · GM2-activator Protein crystal structure · 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 1PU5 · PDBe 1PU5 · UniProt P17900

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