3ZDH: Ls-AChBP

Crystal structure of Ls-AChBP complexed with carbamoylcholine analogue N,N-dimethyl-4-(1-methyl-1H-imidazol-2-yloxy)butan-2-amine. Determined by X-ray diffraction at 2.19 Å resolution. Released 20 Feb 2013.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: LYMNAEA STAGNALIS
Chains: 10
Atoms: 17,357
Mol. weight: 241.23 kDa
Ligands: NAG, XRS
Released: 20 Feb 2013

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

Secondary structure: helices and β-sheets

3ZDH contains 41 α-helices and 154 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, D, E, F and I: 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	150-153	4	2
β-strand	171-184	14	3
β-strand	191-203	13	3

Chains B and J: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	22	1	4
β-strand	25	1	4
α-helix	26	1
β-strand	27-38	12	5
β-strand	42	1	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, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	22	1	7
β-strand	25	1	7
α-helix	26	1
β-strand	27-42	16	8
β-strand	47-59	13	8
α-helix	61-63	3
β-strand	73-77	5	8
α-helix	78-80	3
β-strand	86-88	3	9
β-strand	91	1	8
β-strand	96-97	2	8
β-strand	102-106	5	8
β-strand	110-113	4	8
β-strand	116-122	7	8
β-strand	134-142	9	9
β-strand	150-154	5	8
β-strand	171-184	14	9
β-strand	191-203	13	9

Chain G: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	22	1	19
β-strand	25	1	19
α-helix	26	1
β-strand	27-38	12	20
β-strand	42	1	20
β-strand	47-59	13	20
α-helix	61-63	3
β-strand	73-77	5	20
α-helix	78-80	3
β-strand	86-88	3	21
β-strand	91	1	20
β-strand	96-97	2	20
β-strand	102-106	5	20
β-strand	110-113	4	20
β-strand	116-122	7	20
β-strand	134-142	9	21
β-strand	150-154	5	20
β-strand	171-184	14	21
β-strand	191-203	13	21

Chain H: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	22	1	22
β-strand	25	1	22
α-helix	26	1
β-strand	27-38	12	23
β-strand	42	1	23
β-strand	47-59	13	23
α-helix	61-63	3
β-strand	73-77	5	23
α-helix	78-80	3
β-strand	86-88	3	24
β-strand	91	1	23
β-strand	96-97	2	23
β-strand	102-106	5	23
β-strand	110-113	4	23
β-strand	116-122	7	23
β-strand	134-142	9	24
β-strand	150-154	5	23
α-helix	162-164	3
β-strand	171-184	14	24
β-strand	191-203	13	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine binding protein	A, B, C, D, E, F, G, H, I, J	protein	210	LYMNAEA STAGNALIS	P58154 (AlphaFold model)

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

>3ZDH_1 ACETYLCHOLINE BINDING PROTEIN (chains A, B, C, D, E, F, G, H, I, J)
LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSD
RTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQR
FSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKK
NSVTYSCCPEAYEDVEVSLNFRKKGRSEIL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
XRS	(2R)-N,N-dimethyl-4-(1-methylimidazol-2-yl)oxy-butan-2-amine	C10 H19 N3 O	10

Water and common crystallization additives (SO4) are not listed.

Primary citation

Synthesis, Pharmacology, and Biostructural Characterization of Novel Alpha(4)Beta(2) Nicotinic Acetylcholine Receptor Agonists. Ussing, C.A., Hansen, C.P., Petersen, J.G. et al. J Med Chem (2013) 56:940. DOI 10.1021/JM301409F · 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…
3WTN 2.09 Å, Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with…
4QAC 2.1 Å, X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPLEX WITH…

Browse structure collections

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