7NDV: Acetylcholine-binding protein

Name: PDB 7NDV: X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001888.
Published: 2021-04-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: choline-binding protein

X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001888. Determined by X-ray diffraction at 1.7 Å resolution. Released 7 Apr 2021.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Lymnaea stagnalis
Chains: 10
Atoms: 17,801
Mol. weight: 274.3 kDa
Ligands: NAG, U8Q
Released: 7 Apr 2021

Explore 7NDV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NDV contains 42 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, B, C, D, E, H, I and J: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
β-strand	41	1	1
β-strand	44	1	1
α-helix	45	1
β-strand	46-61	16	2
β-strand	66-78	13	2
α-helix	80-82	3
β-strand	92-96	5	2
α-helix	97-99	3
β-strand	105-107	3	3
β-strand	110	1	2
β-strand	115-116	2	2
β-strand	121-125	5	2
β-strand	129-132	4	2
β-strand	135-141	7	2
β-strand	153-161	9	3
β-strand	169-172	4	2
β-strand	190-203	14	3
β-strand	210-222	13	3

Chain F: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
α-helix	44-45	2
β-strand	46-57	12	16
β-strand	61	1	16
β-strand	66-78	13	16
α-helix	80-82	3
β-strand	92-96	5	16
α-helix	97-99	3
β-strand	105-107	3	17
β-strand	110	1	16
β-strand	115-116	2	16
β-strand	121-125	5	16
β-strand	129-132	4	16
β-strand	135-141	7	16
β-strand	153-161	9	17
β-strand	169-172	4	16
β-strand	190-203	14	17
β-strand	210-222	13	17

Chain G: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
β-strand	41	1	18
β-strand	44	1	18
α-helix	45	1
β-strand	46-61	16	19
β-strand	66-78	13	19
α-helix	80-82	3
β-strand	92-96	5	19
α-helix	97-99	3
β-strand	105-107	3	20
β-strand	110	1	19
β-strand	115-116	2	19
β-strand	121-125	5	19
β-strand	129-132	4	19
β-strand	135-141	7	19
β-strand	153-161	9	20
β-strand	169-172	4	19
α-helix	173-176	4
β-strand	190-202	13	20
β-strand	211-222	12	20
α-helix	223-224	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine-binding protein	A, B, C, D, E, F, G, H, I, J	protein	237	Lymnaea stagnalis	P58154 (AlphaFold model)

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

>7NDV_1 Acetylcholine-binding protein (chains A, B, C, D, E, F, G, H, I, J)
MRRNIFCLACLWIVQACLSLDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEV
NEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQ
LARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDD
SEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSEILGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
U8Q	4-[4-(trifluoromethyl)phenoxy]piperidine	C12 H14 F3 N O	9

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

Primary citation

Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor. Fitzgerald, E.A., Butko, M.T., Boronat, P. et al. Rsc Advances (2021) 11:7527-7537.

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

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…
7PE5 2.1 Å, Crystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP)…

Browse structure collections

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