5AFK: Alpha7-AChBP

alpha7-AChBP in complex with lobeline and fragment 2. Determined by X-ray diffraction at 2.38 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 2.38 Å
Organisms: HOMO SAPIENS, LYMNAEA STAGNALIS
Chains: 5
Atoms: 9,134
Mol. weight: 124.44 kDa
Ligands: 5VU, L0B
Released: 6 May 2015

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

Secondary structure: helices and β-sheets

5AFK contains 24 α-helices and 73 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, 14 β-strands

Element	Residues	Length	Sheet
α-helix	1-11	11
α-helix	25-26	2
β-strand	27-42	16	1
β-strand	47-59	13	1
α-helix	61-63	3
α-helix	67-69	3
β-strand	75-79	5	1
α-helix	80-82	3
β-strand	88-90	3	2
β-strand	93	1	1
β-strand	98-99	2	1
β-strand	104-108	5	1
β-strand	112-115	4	1
β-strand	118-124	7	1
β-strand	136-144	9	2
β-strand	152-156	5	1
β-strand	160	1	1
β-strand	170-182	13	2
β-strand	191-202	12	2

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1-11	11
α-helix	26	1
β-strand	27-42	16	3
β-strand	47-59	13	3
α-helix	61-63	3
β-strand	75-79	5	3
α-helix	80-82	3
β-strand	88-90	3	4
β-strand	93	1	3
β-strand	98-99	2	3
β-strand	104-108	5	3
β-strand	112-115	4	3
β-strand	118-124	7	3
α-helix	128-131	4
β-strand	136-144	9	4
β-strand	152-156	5	3
α-helix	157-158	2
β-strand	170-182	13	4
β-strand	191-202	12	4

Chain C: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1-11	11
β-strand	22	1	5
β-strand	25	1	5
α-helix	26	1
β-strand	27-42	16	6
β-strand	47-59	13	6
α-helix	61-63	3
β-strand	75-79	5	6
α-helix	80-82	3
β-strand	88-90	3	7
β-strand	93	1	6
β-strand	98-99	2	6
β-strand	104-108	5	6
β-strand	112-115	4	6
β-strand	118-124	7	6
α-helix	128-131	4
β-strand	136-144	9	7
β-strand	152-156	5	6
β-strand	170-182	13	7
β-strand	191-202	12	7

Chain D: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	1-11	11
β-strand	22	1	8
β-strand	25	1	8
β-strand	27-42	16	9
β-strand	47-64	18	9
α-helix	67-69	3
β-strand	75-79	5	9
α-helix	80-82	3
β-strand	88-90	3	10
β-strand	93	1	9
β-strand	98-99	2	9
β-strand	104-108	5	9
β-strand	110-115	6	9
β-strand	118-124	7	9
β-strand	136-144	9	10
β-strand	152-156	5	9
β-strand	160	1	9
β-strand	170-182	13	10
β-strand	191-202	12	10

Chain E: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1-11	11
β-strand	22	1	11
β-strand	25	1	11
α-helix	26	1
β-strand	27-42	16	12
β-strand	47-59	13	12
α-helix	67-69	3
β-strand	75-79	5	12
α-helix	80-82	3
β-strand	88-90	3	13
β-strand	93	1	12
β-strand	98-99	2	12
β-strand	104-108	5	12
β-strand	112-115	4	12
β-strand	118-124	7	12
α-helix	128-131	4
β-strand	136-144	9	13
β-strand	152-156	5	12
β-strand	170-182	13	13
β-strand	191-202	12	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7	A, B, C, D, E	protein	205	HOMO SAPIENS, LYMNAEA STAGNALIS	P36544 (AlphaFold model), P58154 (AlphaFold model)

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

>5AFK_1 ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7 (chains A, B, C, D, E)
GEFQRKLYKELVKNYNPDVIPTQRDRPVTVYFSLSLLQIMDVDEKNQVVDVVFWLQMSWT
DHYLQWNVSEYPGVKQVSVPISSLWVPDLAAYNAISKPEVLTPQLALVNSSGHVQYLPSI
RQRFSCDVSGVDTESGATCKLKFGSWTHHSRELDLQMQEADISGYIPYSRFELVGVTQKR
SERFYECCKEPYPDVTFTVTFRKKG

Ligands and cofactors

ID	Name	Formula	Copies
5VU	N-(2,4-difluorophenyl)pyrrolidine-1-carboxamide	C11 H12 F2 N2 O	6
L0B	Alpha-Lobeline	C22 H27 N O2	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…
5AFN 2.15 Å, alpha7-AChBP in complex with lobeline and fragment 5
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

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