6T9R: Aplysia californica AChBP

Aplysia californica AChBP in complex with a cytisine derivative. Determined by X-ray diffraction at 1.72 Å resolution. Released 12 Feb 2020.

Method: X-ray diffraction
Resolution: 1.72 Å
Organism: Aplysia californica
Chains: 10
Atoms: 20,697
Mol. weight: 293.43 kDa
Ligands: PO4, NAG, MXQ
Released: 12 Feb 2020

Explore 6T9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T9R contains 54 α-helices and 150 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 AAA and HHH: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
β-strand	46-61	16	1
β-strand	66-83	18	1
α-helix	86-89	4
β-strand	94-98	5	1
α-helix	99-101	3
β-strand	107-109	3	2
β-strand	112	1	1
α-helix	115-116	2
β-strand	117-118	2	1
β-strand	123-127	5	1
β-strand	129-134	6	1
β-strand	137-143	7	1
β-strand	155-163	9	2
β-strand	171-174	4	1
β-strand	179	1	2
α-helix	180	1
β-strand	181	1	1
β-strand	191-205	15	2
β-strand	208-223	16	2

Chain BBB: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
β-strand	46-61	16	3
β-strand	66-83	18	3
α-helix	86-89	4
β-strand	94-98	5	3
α-helix	99-101	3
β-strand	107-109	3	4
β-strand	112	1	3
α-helix	115-116	2
β-strand	117-118	2	3
β-strand	123-127	5	3
β-strand	129-134	6	3
β-strand	137-143	7	3
β-strand	155-163	9	4
β-strand	171-174	4	3
β-strand	179	1	4
β-strand	181	1	3
β-strand	191-205	15	4
β-strand	208-223	16	4

Chains CCC and III: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-27	7
α-helix	28-32	5
α-helix	35-37	3
β-strand	46-61	16	5
β-strand	66-83	18	5
α-helix	86-89	4
β-strand	94-98	5	5
α-helix	99-101	3
β-strand	107-109	3	6
β-strand	112	1	5
α-helix	115-116	2
β-strand	117-118	2	5
β-strand	123-127	5	5
β-strand	129-134	6	5
β-strand	137-143	7	5
β-strand	155-163	9	6
β-strand	171-174	4	5
β-strand	179	1	6
α-helix	180	1
β-strand	181	1	5
β-strand	191-205	15	6
β-strand	208-223	16	6

Chains DDD, FFF and JJJ: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
α-helix	35-37	3
β-strand	46-61	16	7
β-strand	66-83	18	7
α-helix	86-89	4
β-strand	94-98	5	7
α-helix	99-101	3
β-strand	107-109	3	8
β-strand	112	1	7
α-helix	115-116	2
β-strand	117-118	2	7
β-strand	123-127	5	7
β-strand	129-134	6	7
β-strand	137-143	7	7
β-strand	155-163	9	8
β-strand	171-174	4	7
β-strand	179	1	8
β-strand	181	1	7
β-strand	191-205	15	8
β-strand	208-223	16	8

Chain EEE: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
α-helix	35-36	2
β-strand	46-61	16	9
β-strand	66-83	18	9
α-helix	86-89	4
β-strand	94-98	5	9
α-helix	99-101	3
β-strand	107-109	3	10
β-strand	112	1	9
α-helix	115-116	2
β-strand	117-118	2	9
β-strand	123-127	5	9
β-strand	129-134	6	9
β-strand	137-143	7	9
β-strand	155-163	9	10
β-strand	171-174	4	9
β-strand	179	1	10
α-helix	180	1
β-strand	181	1	9
β-strand	191-205	15	10
β-strand	208-223	16	10

Chain GGG: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
α-helix	35-37	3
β-strand	46-61	16	13
β-strand	66-83	18	13
α-helix	86-88	3
β-strand	94-98	5	13
α-helix	99-101	3
β-strand	107-109	3	14
β-strand	112	1	13
α-helix	115-116	2
β-strand	117-118	2	13
β-strand	123-127	5	13
β-strand	129-134	6	13
β-strand	137-143	7	13
β-strand	155-163	9	14
β-strand	171-174	4	13
β-strand	179	1	14
β-strand	181	1	13
β-strand	191-203	13	14
β-strand	212-223	12	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine binding protein	AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ	protein	249	Aplysia californica	Q8WSF8 (AlphaFold model)

Sequence of entity 1 (AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ), FASTA

>6T9R_1 Acetylcholine binding protein (chains AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ)
MLVSVYLALLVACVGQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKV
DSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLS
PQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGVTCAVKFGSWVYSGFEIDLKTDTDQV
DLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERRAGNGFFRNLFDENLY
FQGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	10
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
MXQ	(1~{R},9~{S})-5-(3-oxidanylpropyl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4…	C14 H20 N2 O2	10

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

Primary citation

The thermodynamic profile and molecular interactions of a C(9)-cytisine derivative-binding acetylcholine-binding protein from Aplysia californica. Davis, S., Rego Campello, H., Gallagher, T. et al. Acta Crystallogr F Struct Biol Commun (2020) 76:74-80. DOI 10.1107/S2053230X20001168 · PubMed

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

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
2WNJ 1.8 Å, Crystal structure of aplysia achbp in complex with dmxba
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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