MolNFT v1 · #48208 · protein

Crystal structure of recombinant full length human butyrylcholinesterase

2PM8: “Crystal structure of recombinant full length human butyrylcholinesterase”. X-ray diffraction, 2 ligands (NAG, SO4), 10 pockets (best druggability 0.78). MolNFT v1 #48208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PM8
Type: protein
Length: 1,060 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cholinesterase
EC: 3.1.1.8
UniProt: P06276
Ligands: NAG, SO4
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cholinesterase (EC 3.1.1.8)	protein	530	35% helix, 17% strand	P06276

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
GOL · Glycerol · additive · 5 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	579	0.78	0.84	46	empty
2	527	0.77	0.84	44	empty
3	786	0.76	0.80	87	empty
4	494	0.65	0.77	47	GOL
5	476	0.65	0.77	47	SO4, GOL

Interfaces

1 interface between chains.

A–B · 643 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation, glycosylation).

Compared structures

2PM8 · Crystal structure of recombinant full length human butyrylcholinesterase · the same entry in another collection · chain A against A, TM-score 1.00
P06276 · AlphaFold monomer V2.0 prediction for cholinesterase (P06276) · 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 P06276
Elsewhere: RCSB PDB 2PM8 · PDBe 2PM8 · UniProt P06276

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