MolNFT v1 · #117750 · protein

Mache-syn TZ2PA5 complex

5EHN · Acetylcholinesterase: “Mache-syn TZ2PA5 complex”. X-ray diffraction, 2 ligands (5NZ, NAG), 14 pockets (best druggability 0.79). MolNFT v1 #117750 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EHN
Type: protein
Length: 1,067 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetylcholinesterase
EC: 3.1.1.7
UniProt: P21836
Ligands: 5NZ, NAG
Pockets: 14 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholinesterase (EC 3.1.1.7)	protein	536	38% helix, 18% strand	P21836
B	Acetylcholinesterase (EC 3.1.1.7)	protein	531	38% helix, 18% strand	P21836

Ligands and binding sites

5NZ · 6-phenyl-5-[5-[3-[2-(1,2,3,4-tetrahydroacridin-9-ylamino)ethyl]-1,2,3-triazol-4-yl]pentyl]phenanthridin-5-ium-3,8-diamine · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
P6G · Hexaethylene glycol · additive · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	413	0.79	0.87	43	5NZ
2	388	0.78	0.87	42	5NZ
3	150	0.67	0.87	19	P6G
4	330	0.60	0.78	38	empty
5	160	0.57	0.82	18	empty

Interfaces

1 interface between chains.

A–B · 935 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5EHN · mAChE-syn TZ2PA5 complex · the same entry in another collection · chain A against A, TM-score 1.00
P21836 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P21836) · a predicted model of the same protein · chain B 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 P21836
Elsewhere: RCSB PDB 5EHN · PDBe 5EHN · UniProt P21836

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