MolNFT v1 · #52075 · protein

Torpedo californica acetylcholinesterase complexed with 2-pam

2VQ6: “Torpedo californica acetylcholinesterase complexed with 2-pam”. X-ray diffraction, 3 ligands (FP1, NAG, SO4), 3 pockets (best druggability 0.75). MolNFT v1 #52075 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VQ6
Type: protein
Length: 529 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: FP1, NAG, SO4
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholinesterase (EC 3.1.1.7)	protein	529	38% helix, 16% strand	P04058

Ligands and binding sites

FP1 · N-hydroxy-1-(1-methylpyridin-2(1H)-ylidene)methanamine · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
SO4 · Sulfate ion · ion · chains A

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

Pockets

3 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	325	0.75	0.86	39	FP1, SO4
2	331	0.57	0.75	34	empty
3	121	0.42	0.76	17	empty

Modifications

Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

2VQ6 · Torpedo californica acetylcholinesterase complexed with 2-PAM · 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 2VQ6 · PDBe 2VQ6 · UniProt P04058

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