2WNJ: Aplysia achbp

Name: PDB 2WNJ: Crystal structure of aplysia achbp in complex with dmxba
Published: 2009-09-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: receptor

Crystal structure of aplysia achbp in complex with dmxba. Determined by X-ray diffraction at 1.8 Å resolution. Released 1 Sept 2009.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: APLYSIA CALIFORNICA
Chains: 5
Atoms: 10,037
Mol. weight: 132.35 kDa
Ligands: ZY7, NAG
Released: 1 Sept 2009

Explore 2WNJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2WNJ contains 23 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: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	1-10	10
α-helix	11-16	6
α-helix	18-19	2
β-strand	24	1	1
β-strand	27	1	1
β-strand	29-44	16	2
β-strand	49-66	18	2
α-helix	69-71	3
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
α-helix	163	1
β-strand	164	1	2
β-strand	174-186	13	3
β-strand	195-206	12	3

Chain B: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	-2-14	17
α-helix	18-20	3
β-strand	24	1	4
β-strand	27	1	4
β-strand	29-44	16	5
β-strand	49-66	18	5
α-helix	69-71	3
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	174-186	13	6
β-strand	195-206	12	6

Chain C: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-5-14	20
α-helix	18-20	3
β-strand	29-44	16	7
β-strand	49-66	18	7
α-helix	69-72	4
β-strand	77-81	5	7
α-helix	82-84	3
β-strand	90-92	3	8
β-strand	95	1	7
β-strand	100-101	2	7
β-strand	106-110	5	7
β-strand	112-117	6	7
β-strand	120-126	7	7
β-strand	138-146	9	8
β-strand	154-157	4	7
β-strand	162	1	8
β-strand	164	1	7
β-strand	174-186	13	8
β-strand	195-206	12	8

Chain D: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-1-10	12
α-helix	11-15	5
α-helix	18-20	3
β-strand	29-44	16	9
β-strand	49-66	18	9
α-helix	69-71	3
β-strand	77-81	5	9
α-helix	82-84	3
β-strand	90-92	3	10
β-strand	95	1	9
β-strand	100-101	2	9
β-strand	106-110	5	9
β-strand	112-117	6	9
β-strand	120-126	7	9
β-strand	138-146	9	10
β-strand	154-157	4	9
β-strand	162	1	10
α-helix	163	1
β-strand	164	1	9
β-strand	174-186	13	10
β-strand	195-206	12	10

Chain E: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	-7-14	22
β-strand	29-44	16	11
β-strand	49-66	18	11
α-helix	69-71	3
β-strand	77-81	5	11
α-helix	82-84	3
β-strand	90-92	3	12
β-strand	95	1	11
β-strand	100-101	2	11
β-strand	106-110	5	11
β-strand	112-117	6	11
β-strand	120-126	7	11
β-strand	138-146	9	12
β-strand	154-157	4	11
β-strand	162	1	12
β-strand	164	1	11
β-strand	174-186	13	12
β-strand	195-206	12	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble acetylcholine receptor	A, B, C, D, E	protein	228	APLYSIA CALIFORNICA	Q8WSF8 (AlphaFold model)

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

>2WNJ_1 SOLUBLE ACETYLCHOLINE RECEPTOR (chains A, B, C, D, E)
DYKDDDDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVD
LVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTH
DGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYAS
SKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERRAGNGFFRNLFD

Ligands and cofactors

ID	Name	Formula	Copies
ZY7	(3E)-3-[(2,4-dimethoxyphenyl)methylidene]-3,4,5,6-tetrahydro-2,3'-bipyridine	C19 H20 N2 O2	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Structural Determinants for Interaction of Partial Agonists with Acetylcholine Binding Protein and Neuronal Alpha7 Nicotinic Acetylcholine Receptor. Hibbs, R.E., Sulzenbacher, G., Shi, J. et al. EMBO J (2009) 28:3040. DOI 10.1038/EMBOJ.2009.227 · PubMed

Other PDB entries of the same protein (UniProt Q8WSF8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6T9R 1.72 Å, Aplysia californica AChBP in complex with a cytisine derivative
2WN9 1.75 Å, Crystal structure of Aplysia ACHBP in complex with 4-0H-DMXBA
2PGZ 1.76 Å, Crystal structure of Cocaine bound to an ACh-Binding Protein
8QTL 1.85 Å, Aplysia californica acetylcholine-binding protein in complex with Spiroimine (-)-4 S
2Y7Y 1.9 Å, Aplysia californica achbp in apo state
4XHE 1.9 Å, Crystal Structure of A-AChBP in complex with pinnatoxin A
4ZK4 1.9 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica…
2XYS 1.91 Å, Crystal structure of Aplysia californica AChBP in complex with strychnine
5TVC 1.93 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica…
3C84 1.94 Å, Crystal structure of a complex of AChBP from aplysia californica and the neonicotinoid…
2YMD 1.96 Å, Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with serotonin…
4WV9 2.0 Å, Crystal structure of acetylcholine binding protein (AChBP) from Aplysia Californica in…

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