MolNFT v1 · #117314 · protein

Acetylcholinesterase methylene blue no peg

5E4J: “Acetylcholinesterase methylene blue no peg”. X-ray diffraction, 5 ligands (DME, NAG, MAN), 5 pockets (best druggability 0.79). MolNFT v1 #117314 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5E4J
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: DME, NAG, MAN, BMA, SO4
Pockets: 5 · best druggability 0.79

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

DME · Decamethonium ion · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 2 copies
BMA · beta-D-mannopyranose · sugar
SO4 · Sulfate ion · ion · 10 copies · 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	339	0.79	0.89	39	DME
2	427	0.62	0.76	34	SO4
3	133	0.43	0.76	21	empty
4	61	0.32	0.76	15	SO4
5	60	0.31	0.76	13	empty

Modifications

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

Compared structures

5E4J · Acetylcholinesterase Methylene Blue no PEG · 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 5E4J · PDBe 5E4J · UniProt P04058

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