9PKY: Glycine receptor, alpha 1

Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 2000 nM ivermectin. Determined by electron microscopy at 2.89 Å resolution. Released 7 Jan 2026.

Method: Electron microscopy
Resolution: 2.89 Å
Organism: Danio rerio
Chains: 5
Atoms: 14,301
Mol. weight: 283.35 kDa
Ligands: IVM, SY9, NAG
Released: 7 Jan 2026

Explore 9PKY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PKY contains 62 α-helices and 71 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: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	34-42	9
β-strand	61-76	16	1
β-strand	81-93	13	1
α-helix	95-97	3
β-strand	107-108	2	1
α-helix	109-110	2
α-helix	111-116	6
β-strand	122-124	3	2
β-strand	127-132	6	1
β-strand	140-144	5	1
β-strand	149-161	13	1
β-strand	173-182	10	2
β-strand	190-194	5	1
β-strand	200-202	3	1
β-strand	211-213	3	2
β-strand	218-221	4	2
β-strand	224-225	2	3
β-strand	230-231	2	3
β-strand	233-242	10	2
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-263	11
α-helix	264-266	3
α-helix	273-294	22
α-helix	306-334	29
α-helix	402-438	37

Chain B: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	36-42	7
α-helix	60	1
β-strand	61-76	16	9
β-strand	81-93	13	9
α-helix	95-97	3
β-strand	106-108	3	9
α-helix	111-116	6
β-strand	122-124	3	10
β-strand	127-132	6	9
β-strand	140-145	6	9
β-strand	149-161	13	9
β-strand	173-182	10	10
β-strand	190-194	5	9
β-strand	200-202	3	9
β-strand	211-213	3	10
β-strand	218-220	3	10
β-strand	224-226	3	11
β-strand	229-231	3	11
β-strand	233-242	10	10
α-helix	243	1
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-262	10
α-helix	264-267	4
α-helix	273-292	20
α-helix	293-295	3
α-helix	306-333	28
α-helix	402-438	37
α-helix	441-443	3

Chain C: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-41	8
α-helix	53	1
α-helix	60	1
β-strand	61-76	16	6
β-strand	81-93	13	6
α-helix	95-97	3
β-strand	106-108	3	6
α-helix	111-116	6
β-strand	122-124	3	7
β-strand	127-131	5	6
β-strand	140-145	6	6
β-strand	149-161	13	6
β-strand	173-182	10	7
β-strand	190-194	5	6
β-strand	200-202	3	6
β-strand	211-221	11	7
β-strand	224-225	2	8
β-strand	230-231	2	8
β-strand	233-242	10	7
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-261	9
α-helix	262-267	6
α-helix	273-293	21
α-helix	306-336	31
α-helix	403-434	32

Chain D: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	34-41	8
α-helix	60	1
β-strand	61-76	16	4
β-strand	81-93	13	4
α-helix	95-97	3
β-strand	106-108	3	4
α-helix	111-116	6
β-strand	122-124	3	5
β-strand	127-132	6	4
β-strand	140-145	6	4
β-strand	149-161	13	4
β-strand	173-186	14	5
β-strand	190-194	5	4
β-strand	200-202	3	4
β-strand	211-220	10	5
β-strand	224-225	2	5
β-strand	230-242	13	5
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-262	10
α-helix	263-267	5
α-helix	273-293	21
α-helix	306-332	27
α-helix	402-438	37

Chain E: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	56-62	7
α-helix	79	1
β-strand	80-95	16	12
β-strand	100-112	13	12
β-strand	126-128	3	12
α-helix	131-136	6
β-strand	142-144	3	13
β-strand	147-150	4	12
β-strand	160-165	6	12
β-strand	169-181	13	12
α-helix	189-191	3
β-strand	193-206	14	13
β-strand	210-214	5	12
β-strand	220-222	3	12
β-strand	230-232	3	13
β-strand	237	1	13
β-strand	244-245	2	13
β-strand	251-263	13	13
α-helix	266-268	3
α-helix	269-273	5
α-helix	274-284	11
α-helix	285-288	4
α-helix	294-315	22
α-helix	316-318	3
α-helix	325-326	2
α-helix	327-351	25
α-helix	467-475	9
α-helix	478-492	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycine receptor, alpha 1	A, B, C, D	protein	458	Danio rerio	B3DHZ5 (AlphaFold model)
Glycine receptor beta subunit 2	E	protein	591	Danio rerio	Q6DC22 (AlphaFold model)

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

>9PKY_1 Glycine receptor, alpha 1 (chains A, B, C, D)
MFALGIYLWETIVFFSLAASQQAAARKAASPMPPSEFLDKLMGKVSGYDARIRPNFKGPP
VNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKP
DLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQL
ESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHL
ERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPK
VSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARQHKELLRFQRRRRHLKEDEAGDGRFSF
AAYGMGPACLQAKDGMAIKGNNNNAPTSTNPPEKTVEEMRKLFISRAKRIDTVSRVAFPL
VFLIFNIFYWITYKIIRSEDIHKQLVPRGSHHHHHHHH

Sequence of entity 2 (E), FASTA

>9PKY_2 Glycine receptor beta subunit 2 (chains E)
MKALKVIFMLLIICLWMEGGFTKEKSAKKWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGG
SGGGSGGGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKENLYFQGEKSAKKGKKKGKQVYC
PSQLSSEDLARVPANSTSNILNKLLITYDPRIRPNFKGIPVEDRVNIFINSFGSIQETTM
DYRVNIFLRQRWNDPRLRLPQDFKSDSLTVDPKMFKCLWKPDLFFANEKSANFHDVTQEN
ILLFIFRNGDVLISMRLSVTLSCPLDLTLFPMDTQRCKMQLESFGYTTDDLQFMWQSGDP
VQMDEIALPQFDIKQEDIEYGNCTKYYAGTGYYTCVEVIFTLRRQVGFYMMGVYAPTLLI
VVLSWLSFWINPDASAARVPLGILSVLSLSSECTSLASELPKVSYVKAIDIWLIACLLFG
FASLVEYAVVQVMLNSPKLLEAERAKIATKEKAEGKTPAKNTINGMGSTPIHVSTLQVTE
TRCKKVCTSKSDLRTNDFSIVGSLPRDFELSNFDCYGKPIEVGSAFSKSQAKNNKKPPPP
KPVIPSAAKRIDLYARALFPFSFLFFNVIYWSVYLENLYFQGTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
IVM	(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-2…	C48 H74 O14	5
SY9	Strychnine	C21 H22 N2 O2	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Structural basis for domain coupling in heteromeric glycine receptors revealed by an atypical allosteric agonist. Gibbs, E., Feddersen, B., Kindig, K.J. et al. Sci Adv (2026) 12:eaeb2036-eaeb2036. DOI 10.1126/sciadv.aeb2036 · PubMed

Other PDB entries of the same protein (UniProt B3DHZ5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PKW 2.86 Å, Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 200…
9PKX 2.86 Å, Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 500…
9PKZ 2.89 Å, Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 0.02…

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