5OBG: Glycine binding protein

Crystal structure of glycine binding protein in complex with strychnine. Determined by X-ray diffraction at 2.0 Å resolution. Released 1 Aug 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Aplysia californica
Chains: 5
Atoms: 9,478
Mol. weight: 146.68 kDa
Ligands: SY9, NAG
Released: 1 Aug 2018

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

Secondary structure: helices and β-sheets

5OBG contains 28 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: 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	1
β-strand	66-83	18	1
α-helix	86-88	3
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	210-223	14	2

Chain B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
β-strand	46-61	16	3
β-strand	66-78	13	3
α-helix	80-82	3
α-helix	86-88	3
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	131-134	4	3
β-strand	137-143	7	3
β-strand	155-163	9	4
β-strand	171-174	4	3
β-strand	179	1	4
α-helix	180	1
β-strand	181	1	3
β-strand	191-204	14	4
β-strand	211-223	13	4

Chain C: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
β-strand	41	1	5
β-strand	44	1	5
β-strand	46-61	16	6
β-strand	66-83	18	6
α-helix	86-89	4
β-strand	94-98	5	6
α-helix	99-101	3
β-strand	107-109	3	7
β-strand	112	1	6
α-helix	115-116	2
β-strand	117-118	2	6
β-strand	123-127	5	6
β-strand	129-134	6	6
β-strand	137-143	7	6
β-strand	155-163	9	7
β-strand	171-174	4	6
β-strand	179	1	7
α-helix	180	1
β-strand	181	1	6
β-strand	191-203	13	7
β-strand	212-223	12	7

Chain D: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
β-strand	46-61	16	8
β-strand	66-83	18	8
α-helix	86-89	4
β-strand	94-98	5	8
α-helix	99-101	3
β-strand	107-109	3	9
β-strand	112	1	8
α-helix	115-116	2
β-strand	117-118	2	8
β-strand	123-127	5	8
β-strand	129-134	6	8
β-strand	137-143	7	8
β-strand	155-163	9	9
β-strand	171-174	4	8
β-strand	179	1	9
β-strand	181	1	8
β-strand	191-204	14	9
β-strand	211-223	13	9

Chain E: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
β-strand	41	1	10
β-strand	44	1	10
β-strand	46-61	16	11
β-strand	66-78	13	11
α-helix	80-82	3
α-helix	86-89	4
β-strand	94-98	5	11
α-helix	99-101	3
β-strand	107-109	3	12
β-strand	112	1	11
α-helix	115-116	2
β-strand	117-118	2	11
β-strand	123-127	5	11
β-strand	131-134	4	11
β-strand	137-143	7	11
β-strand	155-163	9	12
β-strand	171-174	4	11
β-strand	179	1	12
α-helix	180	1
β-strand	181	1	11
β-strand	191-204	14	12
β-strand	211-223	13	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble acetylcholine receptor	A, B, C, D, E	protein	249	Aplysia californica	Q8WSF8 (AlphaFold model)

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

>5OBG_1 Soluble acetylcholine receptor (chains A, B, C, D, E)
MLVSVYLALLVACVGQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFFLQDIVKV
DSSTNEVDLVYYERQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAASSTRPVQVLS
PQIAVVTHDGSVMFSPAQRLSFMCDPTGVDSEEGVTCAVKFESWVYSGFEIDLKTDTDQV
DLSSYYASSKYEILSATQTRQVQHYKGTGEPYIDVNLVVKFRERRAGNGFFRNLFDENLY
FQGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
SY9	Strychnine	C21 H22 N2 O2	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Water and common crystallization additives (EDO, NA, ACT) are not listed.

Primary citation

Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein. Dawson, A., Trumper, P., de Souza, J.O. et al. IUCrJ (2019) 6:1014-1023. DOI 10.1107/S205225251901114X · 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
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…

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