5J5F: Acetylcholine Binding Protein

X-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) in Complex with N4,N4-bis[(pyridin-2-yl)methyl]-6-(thiophen-3-yl)pyrimidine-2,4-diamine. Determined by X-ray diffraction at 2.04 Å resolution. Released 8 Mar 2017.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Lymnaea stagnalis
Chains: 10
Atoms: 19,030
Mol. weight: 255.86 kDa
Ligands: 6GH, NAG, PO4
Released: 8 Mar 2017

Explore 5J5F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J5F contains 42 α-helices and 145 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.

Chain A: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	-6--4	3
α-helix	0-13	14
β-strand	27-42	16	1
β-strand	47-59	13	1
α-helix	61-63	3
β-strand	73-77	5	1
α-helix	78-80	3
β-strand	86-88	3	2
β-strand	91	1	1
β-strand	96-97	2	1
β-strand	102-106	5	1
β-strand	110-113	4	1
β-strand	116-122	7	1
β-strand	134-142	9	2
β-strand	150-153	4	1
α-helix	161-163	3
β-strand	171-185	15	2
β-strand	188-203	16	2

Chains B and I: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	-6--4	3
α-helix	0-13	14
β-strand	27-42	16	3
β-strand	47-59	13	3
α-helix	61-63	3
β-strand	73-77	5	3
α-helix	78-80	3
β-strand	86-88	3	4
β-strand	91	1	3
β-strand	96-97	2	3
β-strand	102-106	5	3
β-strand	110-113	4	3
β-strand	116-122	7	3
β-strand	134-142	9	4
β-strand	150-154	5	3
β-strand	158-159	2	4
β-strand	171-185	15	4
β-strand	188-203	16	4

Chains C, E and J: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	-6--4	3
α-helix	0-13	14
β-strand	22	1	5
β-strand	25	1	5
β-strand	27-42	16	6
β-strand	47-59	13	6
α-helix	61-63	3
β-strand	73-77	5	6
α-helix	78-80	3
β-strand	86-88	3	6
β-strand	91	1	6
β-strand	96-97	2	6
β-strand	102-106	5	6
β-strand	110-113	4	6
β-strand	116-122	7	6
β-strand	134-142	9	6
β-strand	150-154	5	6
β-strand	158-159	2	6
β-strand	171-185	15	6
β-strand	188-203	16	6

Chain D: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	-6--4	3
α-helix	0-13	14
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	159	1	8
β-strand	171-185	15	8
β-strand	188-203	16	8

Chain F: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	-5--2	4
α-helix	0-13	14
β-strand	27-42	16	12
β-strand	47-59	13	12
α-helix	61-63	3
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	171-185	15	13
β-strand	188-203	16	13

Chain G: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	-6--4	3
α-helix	0-13	14
β-strand	27-42	16	14
β-strand	47-59	13	14
α-helix	61-63	3
β-strand	73-77	5	14
α-helix	78-80	3
β-strand	86-88	3	15
β-strand	96-97	2	14
β-strand	102-106	5	14
β-strand	110-113	4	14
β-strand	116-122	7	14
β-strand	124	1	15
β-strand	134-142	9	15
β-strand	150-154	5	14
α-helix	161-163	3
β-strand	171-185	15	15
β-strand	188-203	16	15

Chain H: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	-6--4	3
α-helix	0-13	14
β-strand	22	1	16
β-strand	25	1	16
β-strand	27-42	16	17
β-strand	47-59	13	17
α-helix	61-63	3
β-strand	73-77	5	17
α-helix	78-80	3
β-strand	86-88	3	18
β-strand	91	1	17
β-strand	96-97	2	17
β-strand	102-106	5	17
β-strand	110-113	4	17
β-strand	116-122	7	17
β-strand	134-142	9	18
β-strand	150-154	5	17
β-strand	159	1	18
β-strand	171-185	15	18
β-strand	188-203	16	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine-binding protein	A, B, C, D, E, F, G, H, I, J	protein	218	Lymnaea stagnalis	P58154 (AlphaFold model)

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

>5J5F_1 Acetylcholine-binding protein (chains A, B, C, D, E, F, G, H, I, J)
DYKDDDDKLDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVF
WQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVL
YMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFE
ILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSEIL

Ligands and cofactors

ID	Name	Formula	Copies
6GH	N~4~,N~4~-bis[(pyridin-2-yl)methyl]-6-(thiophen-3-yl)pyrimidine-2,4-diamine	C20 H18 N6 S	10
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
PO4	Phosphate ion	O4 P	11

Water and common crystallization additives (DMS, GOL) are not listed.

Primary citation

Substituted 2-Aminopyrimidines Selective for alpha 7-Nicotinic Acetylcholine Receptor Activation and Association with Acetylcholine Binding Proteins. Kaczanowska, K., Camacho Hernandez, G.A., Bendiks, L. et al. J Am Chem Soc (2017) 139:3676-3684. DOI 10.1021/jacs.6b10746 · 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…
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…
7PE5 2.1 Å, Crystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP)…

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