Research workbench

Torpedo californica acetylcholinesterase complexed with MG+2

Analyse Torpedo californica acetylcholinesterase complexed with MG+2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B38
Type: protein
Length: 532 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetylcholinesterase
EC: 3.1.1.7
UniProt: P04058
Ligands: NAG, FUC, MG, ZN
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholinesterase (EC 3.1.1.7)	protein	532	39% helix, 17% strand	P04058

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
FUC · alpha-L-fucopyranose · sugar · chains A
MG · Magnesium ion · metal · 4 copies · chains A
ZN · Zinc ion · metal · chains A
EDO · 1,2-ethanediol · additive · 7 copies · chains A
GOL · Glycerol · additive · 3 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
PGE · Triethylene glycol · additive · chains A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	337	0.77	0.87	38	PGE, EDO
2	354	0.57	0.75	32	empty
3	100	0.42	0.77	14	GOL
4	70	0.37	0.78	13	empty
5	51	0.34	0.78	14	empty

Modifications

Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

7B38 · Torpedo californica acetylcholinesterase complexed with Mg+2 · the same entry in another collection · chain A against A, TM-score 1.00
P04058 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P04058) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P04058
Elsewhere: RCSB PDB 7B38 · PDBe 7B38 · UniProt P04058

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