9PKZ: Glycine receptor, alpha 1

Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 0.02 mM 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: 14,429
Mol. weight: 283.12 kDa
Ligands: SY9, IVM, NAG
Released: 7 Jan 2026

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

Secondary structure: helices and β-sheets

9PKZ contains 58 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: 13 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	39-42	4
α-helix	53	1
α-helix	60	1
β-strand	61-76	16	1
β-strand	81-93	13	1
α-helix	95-97	3
β-strand	107-109	3	1
α-helix	111-116	6
β-strand	122-123	2	2
β-strand	127-132	6	1
β-strand	140-144	5	1
β-strand	149-161	13	1
α-helix	169-171	3
β-strand	173-178	6	3
β-strand	181-182	2	2
β-strand	190-194	5	1
β-strand	200-202	3	1
β-strand	211-213	3	3
β-strand	218-221	4	3
β-strand	224-225	2	4
β-strand	230-231	2	4
β-strand	233	1	2
β-strand	234-242	9	3
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	402-438	37

Chain B: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	34-41	8
α-helix	53	1
α-helix	60	1
β-strand	61-76	16	11
β-strand	81-93	13	11
β-strand	106-109	4	11
α-helix	111-116	6
β-strand	122-123	2	12
β-strand	127-132	6	11
β-strand	140-145	6	11
β-strand	149-161	13	11
β-strand	173-174	2	13
β-strand	177-182	6	12
β-strand	190-194	5	11
β-strand	200-202	3	11
α-helix	203	1
β-strand	211-213	3	13
β-strand	218-221	4	12
β-strand	224-225	2	14
β-strand	230-231	2	14
β-strand	233-237	5	12
β-strand	240-242	3	13
α-helix	246-247	2
α-helix	248-252	5
α-helix	253-261	9
α-helix	262-266	5
α-helix	273-293	21
α-helix	306-331	26
α-helix	402-438	37

Chain C: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	34-40	7
α-helix	53	1
α-helix	60	1
β-strand	61-76	16	9
β-strand	81-93	13	9
β-strand	106-108	3	9
α-helix	111-116	6
β-strand	122-123	2	10
β-strand	127-132	6	9
β-strand	140-145	6	9
β-strand	149-161	13	9
β-strand	173-186	14	10
β-strand	190-194	5	9
β-strand	200-202	3	9
β-strand	211-220	10	10
β-strand	224-225	2	10
β-strand	230-242	13	10
α-helix	247-250	4
α-helix	252-262	11
α-helix	263-266	4
α-helix	273-294	22
α-helix	306-332	27
α-helix	333-335	3
α-helix	405-434	30

Chain D: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	34-40	7
α-helix	60	1
β-strand	61-65	5	5
β-strand	66	1	6
β-strand	67-69	3	7
β-strand	71-76	6	6
β-strand	81-93	13	6
β-strand	108-109	2	6
β-strand	122-123	2	8
β-strand	127-132	6	6
β-strand	140-144	5	6
β-strand	149-161	13	6
β-strand	173-186	14	8
β-strand	190-194	5	5
β-strand	200-202	3	7
α-helix	203	1
β-strand	212-218	7	8
β-strand	221	1	8
β-strand	224-226	3	8
β-strand	229-241	13	8
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	299-300	2
α-helix	306-332	27
α-helix	402-434	33

Chain E: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	56-63	8
α-helix	72	1
α-helix	79	1
β-strand	80-95	16	15
β-strand	100-112	13	15
α-helix	134-136	3
β-strand	142-143	2	16
β-strand	147-149	3	15
β-strand	160-164	5	15
β-strand	169-176	8	15
β-strand	179-180	2	15
β-strand	193-206	14	16
β-strand	210-214	5	15
β-strand	220-222	3	15
β-strand	230	1	17
β-strand	237	1	16
β-strand	243-246	4	16
β-strand	250-262	13	16
β-strand	263	1	17
α-helix	266-268	3
α-helix	269-273	5
α-helix	274-283	10
α-helix	284-288	5
α-helix	294-315	22
α-helix	327-351	25
α-helix	469-492	24

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

>9PKZ_1 Glycine receptor, alpha 1 (chains A, B, C, D)
MFALGIYLWETIVFFSLAASQQAAARKAASPMPPSEFLDKLMGKVSGYDARIRPNFKGPP
VNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKP
DLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQL
ESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHL
ERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPK
VSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARQHKELLRFQRRRRHLKEDEAGDGRFSF
AAYGMGPACLQAKDGMAIKGNNNNAPTSTNPPEKTVEEMRKLFISRAKRIDTVSRVAFPL
VFLIFNIFYWITYKIIRSEDIHKQLVPRGSHHHHHHHH

Sequence of entity 2 (E), FASTA

>9PKZ_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
SY9	Strychnine	C21 H22 N2 O2	5
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
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	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…
9PKX 2.86 Å, Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 500…
9PKY 2.89 Å, Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 2000…

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