2YMD: Mutant binding protein

Name: PDB 2YMD: Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with serotonin (5-hydroxytryptamine)
Published: 2012-12-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: receptor

Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with serotonin (5-hydroxytryptamine). Determined by X-ray diffraction at 1.96 Å resolution. Released 12 Dec 2012.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: APLYSIA CALIFORNICA
Chains: 10
Atoms: 19,801
Mol. weight: 244.93 kDa
Ligands: PO4, SRO
Released: 12 Dec 2012

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

Secondary structure: helices and β-sheets

2YMD contains 39 α-helices and 152 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.

Chain A: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	16-17	2
β-strand	27-42	16	1
β-strand	47-64	18	1
α-helix	67-70	4
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	110-115	6	1
β-strand	118-124	7	1
β-strand	136-144	9	2
β-strand	152-155	4	1
β-strand	160	1	2
β-strand	162	1	1
β-strand	172-184	13	2
β-strand	193-204	12	2

Chain B: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
β-strand	27-42	16	3
β-strand	47-64	18	3
α-helix	67-70	4
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	110-115	6	3
β-strand	118-124	7	3
β-strand	136-144	9	4
β-strand	152-155	4	3
β-strand	160	1	4
β-strand	162	1	3
β-strand	172-186	15	4
β-strand	189-204	16	4

Chain C: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
β-strand	27-42	16	5
β-strand	47-64	18	5
α-helix	67-70	4
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	152-155	4	5
β-strand	160	1	6
α-helix	161	1
β-strand	162	1	5
β-strand	172-184	13	6
β-strand	193-204	12	6

Chain D: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
β-strand	27-42	16	7
β-strand	47-64	18	7
α-helix	67-70	4
β-strand	75-79	5	7
α-helix	80-82	3
β-strand	88-90	3	8
β-strand	93	1	7
β-strand	98-99	2	7
β-strand	104-108	5	7
β-strand	110-115	6	7
β-strand	118-124	7	7
β-strand	136-144	9	8
β-strand	152-155	4	7
β-strand	160	1	8
β-strand	162	1	7
β-strand	172-184	13	8
β-strand	193-204	12	8

Chain E: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	16-18	3
β-strand	27-42	16	9
β-strand	47-64	18	9
α-helix	67-70	4
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	152-155	4	9
β-strand	160	1	10
α-helix	161	1
β-strand	162	1	9
β-strand	172-184	13	10
α-helix	192	1
β-strand	193-204	12	10

Chain F: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
β-strand	27-42	16	11
β-strand	47-64	18	11
α-helix	67-70	4
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	110-115	6	11
β-strand	118-124	7	11
β-strand	136-144	9	12
β-strand	152-155	4	11
β-strand	160	1	12
β-strand	162	1	11
β-strand	172-186	15	12
β-strand	189-204	16	12
β-strand	208	1	13
β-strand	211	1	13

Chain G: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
β-strand	27-42	16	14
β-strand	47-64	18	14
α-helix	67-70	4
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	152-155	4	14
β-strand	160	1	15
α-helix	161	1
β-strand	162	1	14
β-strand	172-184	13	15
β-strand	193-204	12	15

Chain H: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	16-18	3
β-strand	27-42	16	16
β-strand	47-64	18	16
α-helix	67-70	4
β-strand	75-79	5	16
α-helix	80-82	3
β-strand	88-90	3	17
β-strand	93	1	16
β-strand	98-99	2	16
β-strand	104-108	5	16
β-strand	110-115	6	16
β-strand	118-124	7	16
β-strand	136-144	9	17
β-strand	152-155	4	16
β-strand	160	1	17
β-strand	162	1	16
β-strand	172-184	13	17
β-strand	193-204	12	17

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble acetylcholine receptor	A, B, C, D, E, F, G, H, I, J	protein	212	APLYSIA CALIFORNICA	Q8WSF8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>2YMD_1 SOLUBLE ACETYLCHOLINE RECEPTOR (chains A, B, C, D, E, F, G, H, I, J)
QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKVDSSTNEVDLVYWEQQRWKL
NSLMWDPNEYGNITDFRTSAADIWTPDITAYESTRPVQVLSPQIAVVTHDGSVMFIPAQR
LSFMCDPTGVDSEEGVTCALTFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQT
RQVQHYSCCPEPYIDVNLVVKFRERRAGNGFF

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	10
SRO	Serotonin	C10 H12 N2 O	10

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

Primary citation

Structural Basis of Ligand Recognition in 5-Ht(3) Receptors. Kesters, D., Thompson, A.J., Brams, M. et al. EMBO Rep (2013) 14:49. DOI 10.1038/EMBOR.2012.189 · 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…
4WV9 2.0 Å, Crystal structure of acetylcholine binding protein (AChBP) from Aplysia Californica in…

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