4ZK4: PDB entry 4ZK4

Name: PDB 4ZK4: Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with…
Published: 2015-05-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: acetylcholine binding protein

Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane. Determined by X-ray diffraction at 1.9 Å resolution. Released 13 May 2015.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Aplysia californica, Homo sapiens
Chains: 5
Atoms: 8,496
Mol. weight: 132.27 kDa
Ligands: TII, MG
Released: 13 May 2015

Explore 4ZK4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZK4 contains 17 α-helices and 81 β-strands across 5 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: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	-3-14	18
β-strand	24	1	1
β-strand	27	1	1
β-strand	29-44	16	2
β-strand	49-66	18	2
α-helix	69-72	4
β-strand	77-81	5	2
α-helix	82-84	3
β-strand	90-92	3	3
β-strand	95	1	2
β-strand	100-101	2	2
β-strand	106-110	5	2
β-strand	112-117	6	2
β-strand	120-126	7	2
β-strand	138-146	9	3
β-strand	154-157	4	2
β-strand	162	1	3
β-strand	164	1	2
β-strand	174-187	14	3
β-strand	194-206	13	3

Chain B: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	0-14	15
β-strand	24	1	4
β-strand	27	1	4
β-strand	29-44	16	5
β-strand	49-66	18	5
α-helix	69-72	4
β-strand	77-81	5	5
α-helix	82-84	3
β-strand	90-92	3	6
β-strand	95	1	5
β-strand	100-101	2	5
β-strand	106-110	5	5
β-strand	112-117	6	5
β-strand	120-126	7	5
β-strand	138-146	9	6
β-strand	154-157	4	5
β-strand	162	1	6
β-strand	164	1	5
β-strand	174-187	14	6
β-strand	194-206	13	6

Chain C: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	1-14	14
β-strand	24	1	7
β-strand	27	1	7
β-strand	29-44	16	8
β-strand	49-66	18	8
α-helix	69-72	4
β-strand	77-81	5	8
α-helix	82-84	3
β-strand	90-92	3	9
β-strand	95	1	8
β-strand	100-101	2	8
β-strand	106-110	5	8
β-strand	112-117	6	8
β-strand	120-126	7	8
β-strand	138-146	9	9
β-strand	154-157	4	8
β-strand	162	1	9
β-strand	164	1	8
β-strand	175-187	13	9
β-strand	194-205	12	9

Chain D: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1-13	13
β-strand	29-44	16	10
β-strand	49-66	18	10
α-helix	69-71	3
β-strand	77-81	5	10
α-helix	82-84	3
β-strand	90-92	3	11
β-strand	95	1	10
α-helix	98-99	2
β-strand	100-101	2	10
β-strand	106-110	5	10
β-strand	112-117	6	10
β-strand	120-126	7	10
β-strand	138-146	9	11
β-strand	154-157	4	10
β-strand	162	1	11
β-strand	164	1	10
β-strand	174-187	14	11
β-strand	194-206	13	11

Chain E: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-6-10	17
α-helix	11-15	5
β-strand	29-44	16	12
β-strand	49-66	18	12
α-helix	69-71	3
β-strand	77-81	5	12
α-helix	82-84	3
β-strand	90-92	3	13
β-strand	95	1	12
β-strand	100-101	2	12
β-strand	106-110	5	12
β-strand	112-117	6	12
β-strand	120-126	7	12
β-strand	138-146	9	13
β-strand	154-157	4	12
β-strand	162	1	13
β-strand	164	1	12
β-strand	175-187	13	13
β-strand	194-205	12	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
soluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera	A, B, C, D, E	protein	229	Aplysia californica, Homo sapiens	P32297 (AlphaFold model), Q8WSF8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>4ZK4_1 soluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera (chains A, B, C, D, E)
YKDDDDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDL
VYWEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHD
GSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASS
KYEILSATQYKHDIKYNCCEEIYPDVVLVVKFRERRAGNGFFRNLFDSR

Ligands and cofactors

ID	Name	Formula	Copies
TII	(5R)-1-methyl-7-[5-(propan-2-yloxy)pyridin-3-yl]-1,7-diazaspiro[4.4]nonane	C16 H25 N3 O	2
MG	Magnesium ion	Mg	2

Water and common crystallization additives (PG4, SO4) are not listed.

Primary citation

Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane. Bobango, J., Wu, J., Talley, T.T. To be published.

Other PDB entries of the same protein (UniProt P32297 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5TVC 1.93 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica…
5SYO 2.0 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica…
6PV7 3.34 Å, Human alpha3beta4 nicotinic acetylcholine receptor in complex with nicotine
6PV8 3.87 Å, Human alpha3beta4 nicotinic acetylcholine receptor in complex with AT-1001

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