8G18: Glutamate receptor ionotropic, NMDA 1

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108. Determined by X-ray diffraction at 2.85 Å resolution. Released 1 Mar 2023.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Xenopus laevis, Rattus norvegicus
Chains: 4
Atoms: 11,400
Mol. weight: 170.55 kDa
Ligands: YGW, NAG
Released: 1 Mar 2023

Explore 8G18 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G18 contains 68 α-helices and 73 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, 17 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	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	1
α-helix	93-96	4
α-helix	105-112	8
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-147	4
α-helix	148-157	10
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	277-281	5
α-helix	283-284	2
β-strand	288-292	5	2
α-helix	298-316	19
α-helix	322-326	5
α-helix	335-336	2
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

Chain B: 15 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	33	1
β-strand	34-42	9	5
α-helix	47-51	5
α-helix	56-59	4
β-strand	65-73	9	5
α-helix	78-91	14
β-strand	94-101	8	5
α-helix	107-119	13
β-strand	123-127	5	5
α-helix	128-131	4
β-strand	143-145	3	5
α-helix	150-163	14
β-strand	168-173	6	6
α-helix	179-190	12
β-strand	198-202	5	6
α-helix	215-221	7
β-strand	227-231	5	6
α-helix	234-246	13
β-strand	255-258	4	6
α-helix	260-263	4
α-helix	274	1
β-strand	278-279	2	6
α-helix	289-308	20
α-helix	315-318	4
α-helix	336-339	4
β-strand	343	1	7
β-strand	348	1	7
β-strand	351	1	8
β-strand	357	1	8
β-strand	362-367	6	6
β-strand	373-380	8	6
β-strand	383-386	4	6

Chain C: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	24	1
β-strand	25-33	9	9
α-helix	36-52	17
β-strand	58-62	5	9
β-strand	65-66	2	9
α-helix	71-77	7
α-helix	78-83	6
β-strand	87-92	6	9
α-helix	93-96	4
α-helix	105-112	8
β-strand	118-120	3	9
α-helix	126-129	4
β-strand	137-139	3	9
α-helix	142-143	2
α-helix	144-146	3
α-helix	147-157	11
β-strand	162-167	6	10
β-strand	168	1	11
α-helix	171-184	14
β-strand	211-215	5	10
β-strand	218	1	11
α-helix	226-234	9
β-strand	239-243	5	10
α-helix	246-258	13
β-strand	268-269	2	10
α-helix	273-275	3
α-helix	279-282	4
β-strand	288-292	5	10
α-helix	298-317	20
α-helix	323-326	4
α-helix	335-336	2
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	10
β-strand	381-388	8	10
β-strand	393-395	3	10
α-helix	399-400	2

Chain D: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	14
β-strand	65-68	4	14
β-strand	71-73	3	14
α-helix	78-89	12
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	168-173	6	15
α-helix	179-191	13
β-strand	198-204	7	15
α-helix	215-220	6
β-strand	227-231	5	15
α-helix	234-245	12
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	315-317	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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	385	Xenopus laevis	A0A8J0TPH2 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	363	Rattus norvegicus	Q00960 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8G18_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDL
ISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVP
PYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGXXXXXXXXXXXXXXXX
XXXXXXGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMT
GAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENI
TDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKL
VQVGIFNGSYIIQNDRKIIWPGGET

Sequence of entity 2 (B, D), FASTA

>8G18_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
PPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSD
RKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIE
QQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDD
GDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPS
EFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQ
SNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVW
PRM

Ligands and cofactors

ID	Name	Formula	Copies
YGW	N-(4-{3-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-oxopropoxy}phenyl)methanesulfo…	C20 H23 F2 N3 O4 S	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

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

Primary citation

Novel GluN2B-Selective NMDA Receptor Negative Allosteric Modulator Possesses Intrinsic Analgesic Properties and Enhances Analgesia of Morphine in a Rodent Tail Flick Pain Model. Harris, L.D., Regan, M.C., Myers, S.J. et al. ACS Chem Neurosci (2023) 14:917-935. DOI 10.1021/acschemneuro.2c00779 · PubMed

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