Research workbench

Ache in complex with a bis-(-)-nor-meptazinol derivative

Analyse Ache in complex with a bis-(-)-nor-meptazinol derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2W6C
Type: protein
Length: 528 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: BM4, NAG
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Acetylcholinesterase (EC 3.1.1.7)	protein	528	39% helix, 16% strand	P04058

Ligands and binding sites

BM4 · 3-[(3R)-3-ethyl-1-{9-[(3S)-3-ethyl-3-(3-hydroxyphenyl)azepan-1-yl]nonyl}azepan-3-yl]phenol · ligand · chains X
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains X

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

Pockets

4 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	371	0.79	0.88	40	BM4
2	345	0.57	0.75	32	empty
3	107	0.42	0.77	18	empty
4	52	0.31	0.77	13	empty

Modifications

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

Compared structures

2W6C · Ache in complex with a bis-(-)-nor-meptazinol derivative · the same entry in another collection · chain X against X, TM-score 1.00
P04058 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P04058) · a predicted model of the same protein · chain X 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 2W6C · PDBe 2W6C · UniProt P04058

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