9PKX: Glycine receptor, alpha 1

Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 500 nM ivermectin. Determined by electron microscopy at 2.86 Å resolution. Released 7 Jan 2026.

Method: Electron microscopy
Resolution: 2.86 Å
Organism: Danio rerio
Chains: 5
Atoms: 13,843
Mol. weight: 278.75 kDa
Ligands: NAG, SY9
Released: 7 Jan 2026

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

Secondary structure: helices and β-sheets

9PKX contains 55 α-helices and 72 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, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-42	9
α-helix	60	1
β-strand	61-76	16	1
β-strand	81-93	13	1
α-helix	95-97	3
β-strand	106-108	3	1
α-helix	114-116	3
β-strand	122-123	2	2
β-strand	127-131	5	1
β-strand	140-145	6	1
β-strand	149-161	13	1
β-strand	173-186	14	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	2
β-strand	230-242	13	2
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-262	10
α-helix	263-267	5
α-helix	273-297	25
α-helix	306-333	28
α-helix	402-433	32

Chain B: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	34-42	9
α-helix	60	1
β-strand	61-76	16	8
β-strand	81-93	13	8
α-helix	95-97	3
β-strand	106-109	4	8
α-helix	114-116	3
β-strand	122-124	3	9
β-strand	127-131	5	8
β-strand	140-145	6	8
β-strand	149-161	13	8
β-strand	173-182	10	9
β-strand	190-194	5	8
β-strand	200-202	3	8
β-strand	211-213	3	9
β-strand	218-221	4	9
β-strand	224-225	2	10
β-strand	230-231	2	10
β-strand	233-242	10	9
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-262	10
α-helix	263-267	5
α-helix	273-297	25
α-helix	306-333	28
α-helix	400-434	35

Chain C: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-41	8
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	127-132	6	6
β-strand	140-145	6	6
β-strand	149-161	13	6
β-strand	173-186	14	7
β-strand	190-194	5	6
β-strand	200-202	3	6
β-strand	211-213	3	7
β-strand	218-221	4	7
β-strand	224-225	2	7
β-strand	230-242	13	7
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-262	10
α-helix	263-266	4
α-helix	273-294	22
α-helix	306-333	28
α-helix	403-434	32

Chain D: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	36-41	6
α-helix	53	1
α-helix	60	1
β-strand	61-76	16	3
β-strand	81-93	13	3
α-helix	95-97	3
β-strand	106-109	4	3
α-helix	114-116	3
β-strand	122-124	3	4
β-strand	127-132	6	3
β-strand	140-145	6	3
β-strand	149-161	13	3
β-strand	173-182	10	4
β-strand	190-194	5	3
β-strand	200-202	3	3
β-strand	211-221	11	4
β-strand	224-225	2	5
β-strand	230-231	2	5
β-strand	233-242	10	4
α-helix	245-247	3
α-helix	248-252	5
α-helix	253-262	10
α-helix	263-266	4
α-helix	273-294	22
α-helix	306-332	27
α-helix	402-435	34

Chain E: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	56-63	8
α-helix	79	1
β-strand	80-95	16	11
β-strand	100-112	13	11
β-strand	126-128	3	11
α-helix	131-136	6
β-strand	142-144	3	12
β-strand	147-152	6	11
β-strand	160-165	6	11
β-strand	169-181	13	11
β-strand	193-202	10	12
β-strand	210-214	5	11
β-strand	220-222	3	11
β-strand	230-232	3	12
β-strand	237-239	3	12
β-strand	244-245	2	13
β-strand	251-252	2	13
β-strand	254-263	10	12
α-helix	266-268	3
α-helix	269-273	5
α-helix	274-283	10
α-helix	284-288	5
α-helix	294-318	25
α-helix	327-354	28
α-helix	469-493	25

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

>9PKX_1 Glycine receptor, alpha 1 (chains A, B, C, D)
MFALGIYLWETIVFFSLAASQQAAARKAASPMPPSEFLDKLMGKVSGYDARIRPNFKGPP
VNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKP
DLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQL
ESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHL
ERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPK
VSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARQHKELLRFQRRRRHLKEDEAGDGRFSF
AAYGMGPACLQAKDGMAIKGNNNNAPTSTNPPEKTVEEMRKLFISRAKRIDTVSRVAFPL
VFLIFNIFYWITYKIIRSEDIHKQLVPRGSHHHHHHHH

Sequence of entity 2 (E), FASTA

>9PKX_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
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
SY9	Strychnine	C21 H22 N2 O2	5

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…
9PKY 2.89 Å, Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 2000…
9PKZ 2.89 Å, Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 0.02…

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