9Q3Y: GluN1b-GluN2B ATD

GluN1b-GluN2B ATD in complex with radiprodil. Determined by X-ray diffraction at 2.74 Å resolution. Released 22 Jul 2026.

Method: X-ray diffraction
Resolution: 2.74 Å
Organisms: Xenopus laevis, Rattus norvegicus
Chains: 4
Atoms: 11,408
Mol. weight: 165.9 kDa
Ligands: A1CNW, NAG
Released: 22 Jul 2026

Explore 9Q3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q3Y contains 70 α-helices and 72 β-strands across 4 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: 21 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	24	1
β-strand	25-33	9	1
α-helix	36-52	17
β-strand	58-66	9	1
α-helix	67-68	2
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	1
α-helix	93-95	3
α-helix	105-114	10
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-146	3
α-helix	147-157	11
β-strand	162-168	7	2
α-helix	171-184	14
β-strand	211-218	8	2
α-helix	226-233	8
β-strand	239-243	5	2
α-helix	246-258	13
β-strand	267-269	3	2
α-helix	273-275	3
α-helix	278-282	5
α-helix	283-284	2
β-strand	288-292	5	2
α-helix	298-316	19
α-helix	323-326	4
α-helix	339-347	9
β-strand	351-354	4	3
β-strand	357-359	3	3
β-strand	360-361	2	4
β-strand	367-368	2	4
β-strand	372-378	7	2
β-strand	381-388	8	2
β-strand	393-395	3	2
α-helix	399-400	2
β-strand	402	1	5
β-strand	406	1	5

Chain B: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	6
α-helix	47-53	7
β-strand	65-73	9	6
α-helix	78-91	14
β-strand	94-101	8	6
α-helix	107-119	13
β-strand	123-127	5	6
α-helix	128-131	4
β-strand	143-145	3	6
α-helix	150-163	14
β-strand	168-174	7	7
α-helix	179-190	12
β-strand	198-205	8	7
α-helix	215-220	6
β-strand	227-231	5	7
α-helix	234-246	13
β-strand	255-258	4	7
α-helix	260-263	4
α-helix	274	1
β-strand	278-281	4	7
α-helix	289-311	23
α-helix	315-318	4
α-helix	336-339	4
β-strand	343	1	8
β-strand	348	1	8
β-strand	351	1	9
β-strand	356	1	6
β-strand	357	1	9
β-strand	362-367	6	7
β-strand	373-380	8	7
β-strand	383-386	4	7

Chain C: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	24	1
β-strand	25-33	9	10
α-helix	36-52	17
β-strand	58-66	9	10
α-helix	67-68	2
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	10
α-helix	93-95	3
α-helix	105-114	10
β-strand	118-120	3	10
α-helix	126-129	4
β-strand	137-139	3	10
α-helix	144-147	4
α-helix	148-157	10
β-strand	162-168	7	11
α-helix	171-184	14
β-strand	211-218	8	11
α-helix	226-234	9
β-strand	239-243	5	11
α-helix	246-258	13
β-strand	267-270	4	11
α-helix	273-275	3
α-helix	278-282	5
α-helix	283-284	2
β-strand	288-292	5	11
α-helix	298-316	19
α-helix	323-326	4
α-helix	339-347	9
β-strand	351-354	4	12
β-strand	357-359	3	12
β-strand	360-361	2	13
β-strand	367-368	2	13
β-strand	372-378	7	11
β-strand	381-388	8	11
β-strand	393-395	3	11
α-helix	399-400	2

Chain D: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	14
α-helix	47-54	8
α-helix	57-59	3
β-strand	65-73	9	14
α-helix	78-91	14
β-strand	94-101	8	14
α-helix	107-119	13
β-strand	123-127	5	14
α-helix	128-131	4
β-strand	143-145	3	14
α-helix	150-163	14
β-strand	168-174	7	15
α-helix	179-191	13
β-strand	198-205	8	15
α-helix	215-220	6
β-strand	227-231	5	15
α-helix	234-246	13
β-strand	255-258	4	15
α-helix	260-263	4
α-helix	274	1
β-strand	278-281	4	15
α-helix	289-311	23
α-helix	326-328	3
α-helix	336-339	4
β-strand	343-344	2	16
β-strand	347-348	2	16
β-strand	351	1	17
β-strand	356	1	14
β-strand	357	1	17
β-strand	362-367	6	15
β-strand	373-380	8	15
β-strand	383-386	4	15
α-helix	391-393	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A	protein	359	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	363	Rattus norvegicus	Q00960 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 1	C	protein	358	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9Q3Y_1 Glutamate receptor ionotropic, NMDA 1 (chains A)
DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDL
ISSQVYAILVSHPPALTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSH
QALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGGPKADKVLQFEPGTKNLTAL
LLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGII
GLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMS
SKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGET

Sequence of entity 2 (B, D), FASTA

>9Q3Y_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
PPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSD
RKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIE
QQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDD
GDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPS
EFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQ
SNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVW
PRM

Sequence of entity 3 (C), FASTA

>9Q3Y_3 Glutamate receptor ionotropic, NMDA 1 (chains C)
DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDL
ISSQVYAILVSHPPAHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYS
HQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGPKADKVLQFEPGTKNLTAL
LLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGII
GLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMS
SKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGE

Ligands and cofactors

ID	Name	Formula	Copies
A1CNW	radiprodil	C21 H20 F N3 O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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

Primary citation

Inhibition of GluN2B-containing N-methyl-D-aspartate receptors by radiprodil. Banke, T.G., Regan, M.C., Perszyk, R.E. et al. Brain (2026) 149:976-992. DOI 10.1093/brain/awaf355 · PubMed

Other PDB entries of the same protein (UniProt A0A1L8F5J9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3QEK 2.0 Å, Crystal structure of amino terminal domain of the NMDA receptor subunit GluN1
6E7R 2.1 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7U 2.27 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7T 2.31 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7X 2.58 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
3QEL 2.6 Å, Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and…
6E7V 2.6 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7W 2.67 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
5TQ0 2.7 Å, Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and…
6E7S 2.72 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
5EWM 2.76 Å, Crystal structure of amino terminal domains of the nmda receptor subunit GLUN1 and…
5EWJ 2.77 Å, Crystal structure of amino terminal domains of the nmda receptor subunit GLUN1 and…

Browse structure collections

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