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Crystal structure of mache-Y337A-TZ2PA6 anti complex (1 mth)

Analyse Crystal structure of mache-Y337A-TZ2PA6 anti complex (1 mth) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XUF
Type: protein
Length: 1,065 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: TZ4, NAG
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholinesterase (EC 3.1.1.7)	protein	534	38% helix, 18% strand	P21836
B	Acetylcholinesterase (EC 3.1.1.7)	protein	531	39% helix, 19% strand	P21836

Ligands and binding sites

TZ4 · 3,8-diamino-6-phenyl-5-[6-[1-[2-[(1,2,3,4-tetrahydro-9-acridinyl)amino]ethyl]-1H-1,2,3-triazol-4-yl]hexyl]-phenanthridinium · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	353	0.81	0.90	38	TZ4
2	329	0.81	0.90	41	TZ4
3	154	0.65	0.86	18	P6G
4	336	0.61	0.78	38	empty
5	184	0.58	0.81	21	empty

Interfaces

1 interface between chains.

A–B · 911 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

2XUF · Crystal structure of mache-Y337A-TZ2PA6 anti complex (1 mth) · 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 2XUF · PDBe 2XUF · UniProt P21836

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