3WTN: Lymnaea stagnalis Acetylcholine Binding Protein

Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid. Determined by X-ray diffraction at 2.09 Å resolution. Released 4 Feb 2015.

Method: X-ray diffraction
Resolution: 2.09 Å
Organism: Lymnaea stagnalis
Chains: 10
Atoms: 18,230
Mol. weight: 250.44 kDa
Ligands: N2Y, CD
Released: 4 Feb 2015

Explore 3WTN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WTN contains 37 α-helices and 149 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and H: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	22	1	1
β-strand	25	1	1
α-helix	26	1
β-strand	27-42	16	2
β-strand	47-59	13	2
α-helix	61-63	3
β-strand	73-77	5	2
α-helix	78-80	3
β-strand	86-88	3	3
β-strand	91	1	2
β-strand	96-97	2	2
β-strand	102-106	5	2
β-strand	110-113	4	2
β-strand	116-122	7	2
β-strand	134-142	9	3
β-strand	150-154	5	2
β-strand	171-184	14	3
β-strand	191-203	13	3

Chain B: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	22	1	4
β-strand	25	1	4
β-strand	27-42	16	5
β-strand	47-59	13	5
α-helix	61-63	3
β-strand	73-77	5	5
α-helix	78-80	3
β-strand	86-88	3	6
β-strand	91	1	5
β-strand	96-97	2	5
β-strand	102-106	5	5
β-strand	110-113	4	5
β-strand	116-122	7	5
β-strand	134-142	9	6
β-strand	150-153	4	5
β-strand	171-184	14	6
β-strand	191-203	13	6

Chain C: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	26	1
β-strand	27-42	16	7
β-strand	47-59	13	7
α-helix	61-63	3
β-strand	73-77	5	7
α-helix	78-80	3
β-strand	86-88	3	8
β-strand	91	1	7
β-strand	96-97	2	7
β-strand	102-106	5	7
β-strand	110-113	4	7
β-strand	116-122	7	7
β-strand	134-142	9	8
β-strand	150-154	5	7
β-strand	171-184	14	8
β-strand	191-203	13	8

Chain D: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	22	1	9
β-strand	25	1	9
α-helix	26	1
β-strand	27-38	12	10
β-strand	42	1	10
β-strand	47-59	13	10
α-helix	61-63	3
β-strand	73-77	5	10
α-helix	78-80	3
β-strand	86-88	3	11
β-strand	91	1	10
β-strand	96-97	2	10
β-strand	102-106	5	10
β-strand	110-113	4	10
β-strand	116-122	7	10
β-strand	134-142	9	11
β-strand	150-154	5	10
β-strand	171-183	13	11
β-strand	192-203	12	11

Chain E: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	26	1
β-strand	27-42	16	12
β-strand	47-59	13	12
β-strand	73-77	5	12
α-helix	78-80	3
β-strand	86-88	3	13
β-strand	91	1	12
β-strand	96-97	2	12
β-strand	102-106	5	12
β-strand	110-113	4	12
β-strand	116-122	7	12
β-strand	134-142	9	13
β-strand	150-154	5	12
β-strand	171-177	7	13
β-strand	180-184	5	13
β-strand	191-203	13	13

Chain F: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	22	1	14
β-strand	25	1	14
α-helix	26	1
β-strand	27-42	16	15
β-strand	47-59	13	15
β-strand	73-77	5	15
α-helix	78-80	3
β-strand	86-88	3	16
β-strand	91	1	15
β-strand	96-97	2	15
β-strand	102-106	5	15
β-strand	110-113	4	15
β-strand	116-122	7	15
β-strand	134-142	9	16
β-strand	150-154	5	15
β-strand	171-184	14	16
β-strand	191-203	13	16

Chain G: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	22	1	17
β-strand	25	1	17
α-helix	26	1
β-strand	27-42	16	18
β-strand	47-59	13	18
α-helix	61-63	3
β-strand	73-77	5	18
α-helix	78-80	3
β-strand	86-88	3	19
β-strand	91	1	18
β-strand	96-97	2	18
β-strand	102-106	5	18
β-strand	110-113	4	18
β-strand	116-122	7	18
β-strand	134-142	9	19
β-strand	150-154	5	18
β-strand	171-184	14	19
β-strand	191-203	13	19

Chain I: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	22	1	23
β-strand	25	1	23
α-helix	26	1
β-strand	27-38	12	24
β-strand	42	1	24
β-strand	47-59	13	24
α-helix	61-63	3
β-strand	73-77	5	24
α-helix	78-80	3
β-strand	86-88	3	25
β-strand	91	1	24
β-strand	96-97	2	24
β-strand	102-106	5	24
β-strand	110-113	4	24
β-strand	116-122	7	24
β-strand	134-142	9	25
β-strand	150-154	5	24
β-strand	171-184	14	25
β-strand	191-203	13	25

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine-binding protein	A, B, C, D, E, F, G, H, I, J	protein	214	Lymnaea stagnalis	P58154 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>3WTN_1 Acetylcholine-binding protein (chains A, B, C, D, E, F, G, H, I, J)
EAEAADRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQT
TWSDRTLAWDSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPS
IRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDV
TQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSEIL

Ligands and cofactors

ID	Name	Formula	Copies
N2Y	(2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine	C9 H11 Cl N4	10
CD	Cadmium ion	Cd	54

Water and common crystallization additives (NA) are not listed.

Primary citation

Studies on an acetylcholine binding protein identify a basic residue in loop G on the beta 1 strand as a new structural determinant of neonicotinoid actions. Ihara, M., Okajima, T., Yamashita, A. et al. Mol Pharmacol (2014) 86:736-746. DOI 10.1124/mol.114.094698 · PubMed

Other PDB entries of the same protein (UniProt P58154 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7NDV 1.7 Å, X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001888.
4ZK1 1.75 Å, Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein (LsAChBP) in…
4ZJT 1.85 Å, X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (LsAChBP) in…
4ZRU 1.9 Å, X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) in…
8P11 1.9 Å, X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL003044.
7NDP 2.0 Å, X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001856.
7PD6 2.0 Å, Crystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP)…
7PE6 2.01 Å, Crystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP)…
5J5G 2.04 Å, X-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) in Complex with…
5J5F 2.04 Å, X-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) in Complex with…
4QAC 2.1 Å, X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPLEX WITH…
7PE5 2.1 Å, Crystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP)…

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