MolNFT v1 · #112653 · protein

X-ray crystal structure of lymnaea stagnalis acetylcholine binding protein (ls-achbp) in complex with 3-[2-[(2S)-pyrrolidin-2- YL]ETHYNYL]PYRIDINE (ti-5180)

4ZRU · Acetylcholine-binding protein: “X-ray crystal structure of lymnaea stagnalis acetylcholine binding protein (ls-achbp) in complex with…”. X-ray diffraction, 2 ligands (TI9, PO4), 20 pockets (best druggability 0.70). MolNFT v1 #112653…

PDB: 4ZRU
Type: protein
Length: 2,054 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetylcholine-binding protein
UniProt: P58154
Ligands: TI9, PO4
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 10 distinct chains · 9% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholine-binding protein	protein	211	11% helix, 49% strand	P58154
B	Acetylcholine-binding protein	protein	209	10% helix, 49% strand	P58154
C	Acetylcholine-binding protein	protein	203	8% helix, 51% strand	P58154
D	Acetylcholine-binding protein	protein	206	9% helix, 50% strand	P58154
E	Acetylcholine-binding protein	protein	204	9% helix, 50% strand	P58154
F	Acetylcholine-binding protein	protein	211	9% helix, 50% strand	P58154
G	Acetylcholine-binding protein	protein	201	10% helix, 50% strand	P58154
H	Acetylcholine-binding protein	protein	203	9% helix, 46% strand	P58154
I	Acetylcholine-binding protein	protein	203	9% helix, 51% strand	P58154
J	Acetylcholine-binding protein	protein	203	10% helix, 50% strand	P58154

Ligands and binding sites

TI9 · 3-[(2S)-pyrrolidin-2-ylethynyl]pyridine · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
PO4 · Phosphate ion · ion · 10 copies · chains A, B, E, C, D, F, J, G, H, I

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	155	0.70	0.89	28	TI9
2	155	0.69	0.89	26	TI9
3	634	0.68	0.77	67	empty
4	138	0.68	0.88	23	TI9
5	140	0.67	0.88	24	TI9

Interfaces

20 interfaces between chains.

A–E · 1642 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1616 Å² buried · 25 hydrogen bonds · protein-protein
F–J · 1592 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 1534 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1502 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

4ZRU · X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) in… · the same entry in another collection · chain J against J, TM-score 1.00
P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 P58154
Elsewhere: RCSB PDB 4ZRU · PDBe 4ZRU · UniProt P58154

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