5AFN: Alpha7-AChBP

alpha7-AChBP in complex with lobeline and fragment 5. Determined by X-ray diffraction at 2.15 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Homo sapiens, Lymnaea stagnalis
Chains: 5
Atoms: 9,647
Mol. weight: 125.28 kDa
Ligands: NAG, BMA, MAN, L0B
Released: 6 May 2015

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

Secondary structure: helices and β-sheets

5AFN contains 19 α-helices and 79 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: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	1-11	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	75-79	5	2
α-helix	80-82	3
β-strand	88-90	3	3
β-strand	93	1	2
β-strand	98-99	2	2
β-strand	104-108	5	2
β-strand	112-115	4	2
β-strand	118-124	7	2
α-helix	128-131	4
β-strand	136-144	9	3
β-strand	152-156	5	2
β-strand	160	1	2
β-strand	170-182	13	3
β-strand	191-202	12	3

Chain B: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	1-10	10
β-strand	22	1	4
β-strand	25	1	4
α-helix	26	1
β-strand	27-42	16	5
β-strand	47-64	18	5
β-strand	75-79	5	5
α-helix	80-82	3
β-strand	88-90	3	6
β-strand	93	1	5
β-strand	98-99	2	5
β-strand	104-108	5	5
β-strand	110-115	6	5
β-strand	118-124	7	5
β-strand	136-144	9	6
β-strand	152-156	5	5
β-strand	160	1	5
β-strand	170-182	13	6
β-strand	191-202	12	6

Chain C: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	1-11	11
β-strand	22	1	7
β-strand	25	1	7
α-helix	26	1
β-strand	27-42	16	8
β-strand	47-64	18	8
β-strand	75-79	5	8
α-helix	80-82	3
β-strand	88-90	3	9
β-strand	93	1	8
β-strand	98-99	2	8
β-strand	104-108	5	8
β-strand	110-115	6	8
β-strand	118-124	7	8
β-strand	136-144	9	9
β-strand	152-156	5	8
β-strand	160	1	8
β-strand	170-182	13	9
β-strand	191-202	12	9

Chain D: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	1-13	13
β-strand	22	1	10
β-strand	25	1	10
α-helix	26	1
β-strand	27-42	16	11
β-strand	47-59	13	11
α-helix	61-63	3
β-strand	75-79	5	11
α-helix	80-82	3
β-strand	88-90	3	12
β-strand	93	1	11
β-strand	98-99	2	11
β-strand	104-108	5	11
β-strand	112-115	4	11
β-strand	118-124	7	11
β-strand	136-144	9	12
β-strand	152-156	5	11
β-strand	160	1	11
β-strand	170-182	13	12
β-strand	191-202	12	12

Chain E: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1-10	10
β-strand	22	1	13
β-strand	25	1	13
α-helix	26	1
β-strand	27-42	16	14
β-strand	47-64	18	14
α-helix	67-69	3
β-strand	75-79	5	14
α-helix	80-82	3
β-strand	88-90	3	15
β-strand	93	1	14
β-strand	98-99	2	14
β-strand	104-108	5	14
β-strand	110-115	6	14
β-strand	118-124	7	14
β-strand	136-144	9	15
β-strand	152-156	5	14
β-strand	170-182	13	15
β-strand	191-202	12	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7	A, B, C, D, E	protein	207	Homo sapiens, Lymnaea stagnalis	P36544 (AlphaFold model), P58154 (AlphaFold model)

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

>5AFN_1 ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7 (chains A, B, C, D, E)
GEFQRKLYKELVKNYNPDVIPTQRDRPVTVYFSLSLLQIMDVDEKNQVVDVVFWLQMSWT
DHYLQWNVSEYPGVKQVSVPISSLWVPDLAAYNAISKPEVLTPQLALVNSSGHVQYLPSI
RQRFSCDVSGVDTESGATCKLKFGSWTHHSRELDLQMQEADISGYIPYSRFELVGVTQKR
SERFYECCKEPYPDVTFTVTFRKKGRS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
BMA	beta-D-mannopyranose	C6 H12 O6	1
MAN	alpha-D-mannopyranose	C6 H12 O6	1
L0B	Alpha-Lobeline	C22 H27 N O2	5
OJD	(4R)-4-(2-phenylethyl)pyrrolidin-2-one	C12 H15 N O	5

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

Primary citation

Molecular Blueprint of Allosteric Binding Sites in a Homologue of the Agonist-Binding Domain of the Alpha7 Nicotinic Acetylcholine Receptor. Spurny, R., Debaveye, S., Farinha, A. et al. Proc Natl Acad Sci U S A (2015) 112:E2543. DOI 10.1073/PNAS.1418289112 · PubMed

Other PDB entries of the same protein (UniProt P36544 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P1H 1.95 Å, Crystal structure of the chimera of human 14-3-3 zeta and phosphorylated cytoplasmic…
9QTO 2.16 Å, Human alpha7 nicotinic receptor in complex with the E6 nanobody
8V8A 2.19 Å, Alpha7-nicotinic acetylcholine receptor time resolved bound to epibatidine and…
5AFJ 2.2 Å, alpha7-AChBP in complex with lobeline and fragment 1
9QTN 2.28 Å, Human alpha7 nicotinic receptor in complex with the F1 nanobody
8C9X 2.3 Å, human alpha7 nicotinic receptor in complex with the C4 nanobody
8UT1 2.3 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine
8UTB 2.3 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine and NS-1738
8UZJ 2.3 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine and ivermectin
8V88 2.3 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine and GAT107
8V80 2.34 Å, Alpha7-nicotinic acetylcholine receptor bound to epibatidine and (-)-TQS
5AFK 2.38 Å, alpha7-AChBP in complex with lobeline and fragment 2

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