9OBX: Glutamate/glycine and Ca2+-bound GluN1a/2B NMDAR

glutamate/glycine and Ca2+-bound GluN1a/2B NMDAR. Determined by electron microscopy at 2.59 Å resolution. Released 6 May 2026.

Method: Electron microscopy
Resolution: 2.59 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 21,017
Mol. weight: 383.89 kDa
Ligands: GLY, GLU
Released: 6 May 2026

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

Secondary structure: helices and β-sheets

9OBX contains 133 α-helices and 161 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: 35 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	1
α-helix	36-51	16
α-helix	66-68	3
α-helix	71-85	15
β-strand	89	1	1
β-strand	90-91	2	2
α-helix	105-114	10
β-strand	118-119	2	2
α-helix	127-129	3
β-strand	137-138	2	2
α-helix	148-158	11
β-strand	163-168	6	3
α-helix	171-186	16
β-strand	193-197	5	3
α-helix	205-212	8
β-strand	216	1	4
β-strand	218-221	4	3
α-helix	225-237	13
β-strand	246-249	4	3
α-helix	251-254	4
α-helix	257-260	4
α-helix	262-263	2
β-strand	267-271	5	3
α-helix	277-297	21
α-helix	319-327	9
β-strand	339-340	2	5
β-strand	346-347	2	5
β-strand	351-357	7	3
β-strand	360-367	8	3
β-strand	372-374	3	3
α-helix	382-384	3
β-strand	392	1	4
β-strand	397-402	6	6
β-strand	405	1	7
β-strand	409	1	7
β-strand	410-413	4	6
α-helix	414-415	2
β-strand	424	1	8
α-helix	429	1
β-strand	430	1	8
α-helix	431-432	2
β-strand	434-439	6	6
β-strand	450-456	7	6
α-helix	458-470	13
β-strand	473-478	6	6
β-strand	487-489	3	9
β-strand	496-498	3	9
α-helix	500-506	7
β-strand	512-513	2	6
α-helix	517	1
β-strand	518	1	10
α-helix	519	1
α-helix	521-524	4
β-strand	527-529	3	6
β-strand	534	1	10
β-strand	538-543	6	11
β-strand	558	1	12
α-helix	560-582	23
α-helix	603-615	13
α-helix	627-656	30
α-helix	670-673	4
β-strand	681-682	2	11
β-strand	684	1	13
α-helix	688-695	8
α-helix	697-699	3
α-helix	700-707	8
β-strand	711	1	13
α-helix	714-722	9
β-strand	728-732	5	11
α-helix	733-742	10
β-strand	746-753	8	11
β-strand	758	1	10
β-strand	761-763	3	6
α-helix	769-782	14
α-helix	784-792	9
β-strand	808	1	14
α-helix	814-837	24

Chain B: 31 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	15
α-helix	47-52	6
α-helix	53-55	3
β-strand	67-73	7	15
α-helix	78-89	12
β-strand	94-97	4	15
β-strand	100	1	15
α-helix	107-118	12
β-strand	123-124	2	15
α-helix	128-131	4
β-strand	143-144	2	15
α-helix	150-163	14
β-strand	168-173	6	16
α-helix	179-190	12
β-strand	195	1	17
β-strand	198-199	2	16
α-helix	213-220	8
β-strand	227-231	5	16
α-helix	236-247	12
β-strand	255-258	4	16
α-helix	260-263	4
α-helix	274	1
β-strand	277-282	6	16
α-helix	289-310	22
α-helix	333-337	5
β-strand	343-344	2	18
β-strand	347-348	2	18
β-strand	362-367	6	16
β-strand	373-379	7	16
β-strand	384-386	3	16
β-strand	405-410	6	19
β-strand	418-420	3	19
α-helix	421-423	3
β-strand	430	1	17
β-strand	434-439	6	19
β-strand	452-458	7	19
α-helix	460-472	13
β-strand	475-480	6	19
β-strand	489-490	2	20
β-strand	493-494	2	20
α-helix	496-502	7
β-strand	508-510	3	19
β-strand	514	1	21
α-helix	517-520	4
β-strand	524-525	2	19
β-strand	530-532	3	21
β-strand	534-539	6	22
α-helix	540-541	2
β-strand	554	1	23
α-helix	556-578	23
α-helix	602-613	12
α-helix	626-655	30
α-helix	669-672	4
α-helix	680-681	2
β-strand	683-684	2	22
α-helix	690-698	9
α-helix	700-706	7
α-helix	707-709	3
α-helix	714-723	10
β-strand	728-732	5	22
α-helix	733-740	8
β-strand	748-750	3	22
β-strand	760-762	3	21
β-strand	765-766	2	19
α-helix	772-785	14
α-helix	788-796	9
β-strand	813	1	12
α-helix	820-842	23

Chain C: 37 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	24
α-helix	36-51	16
β-strand	64	1	24
α-helix	66-68	3
α-helix	71-85	15
β-strand	87-91	5	24
α-helix	105-114	10
β-strand	118-119	2	24
α-helix	127-129	3
β-strand	138	1	24
α-helix	144-147	4
α-helix	148-158	11
β-strand	164-168	5	25
α-helix	171-186	16
β-strand	194-197	4	25
α-helix	205-212	8
β-strand	216	1	26
β-strand	218-222	5	25
α-helix	225-237	13
β-strand	246-249	4	25
α-helix	251-254	4
α-helix	258-261	4
α-helix	262-263	2
β-strand	267-271	5	25
α-helix	277-297	21
α-helix	319-327	9
β-strand	340	1	27
β-strand	346	1	27
β-strand	351-357	7	25
β-strand	360-363	4	25
β-strand	365-367	3	28
β-strand	372-374	3	28
α-helix	382-384	3
β-strand	392	1	26
β-strand	397-402	6	29
β-strand	405	1	30
β-strand	409	1	30
β-strand	410-413	4	29
α-helix	414-415	2
β-strand	424	1	31
α-helix	429	1
β-strand	430	1	31
α-helix	431-432	2
β-strand	434-438	5	29
β-strand	451-456	6	29
α-helix	458-470	13
β-strand	473-478	6	29
β-strand	487-489	3	32
β-strand	496-498	3	32
α-helix	500-506	7
β-strand	512-513	2	29
α-helix	517	1
β-strand	518	1	33
α-helix	519	1
α-helix	521-524	4
β-strand	527-529	3	29
β-strand	534	1	33
β-strand	538-543	6	34
β-strand	558	1	35
α-helix	560-581	22
α-helix	603-615	13
α-helix	627-656	30
α-helix	670-673	4
β-strand	676	1	36
β-strand	679	1	36
β-strand	681-682	2	34
β-strand	684	1	37
α-helix	688-694	7
α-helix	697-699	3
α-helix	700-707	8
β-strand	711	1	37
α-helix	714-722	9
β-strand	728-732	5	34
α-helix	733-742	10
β-strand	746-753	8	34
β-strand	758	1	33
β-strand	761-763	3	29
α-helix	769-782	14
α-helix	784-792	9
α-helix	806-807	2
β-strand	808	1	23
α-helix	814-837	24

Chain D: 30 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	38
α-helix	47-52	6
α-helix	54-56	3
β-strand	68-73	6	38
α-helix	78-89	12
β-strand	94-97	4	38
β-strand	100	1	38
α-helix	108-118	11
β-strand	123-124	2	38
α-helix	128-131	4
β-strand	143-144	2	38
α-helix	150-163	14
β-strand	168-173	6	39
α-helix	179-190	12
β-strand	195	1	40
β-strand	198-199	2	39
α-helix	213-220	8
β-strand	227-231	5	39
α-helix	236-247	12
β-strand	255-258	4	39
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	39
α-helix	289-310	22
α-helix	324-326	3
α-helix	333-337	5
β-strand	343-344	2	41
β-strand	347-348	2	41
β-strand	361-367	7	39
β-strand	373-380	8	39
β-strand	384-386	3	39
β-strand	405-410	6	42
β-strand	418-421	4	42
α-helix	422-423	2
β-strand	430	1	40
β-strand	434-439	6	42
β-strand	452-458	7	42
α-helix	460-472	13
β-strand	475-480	6	42
β-strand	489-490	2	43
β-strand	493-494	2	43
α-helix	496-502	7
β-strand	508-510	3	42
β-strand	514	1	44
α-helix	519-521	3
β-strand	524-525	2	42
β-strand	530-532	3	44
β-strand	534-539	6	45
β-strand	554	1	14
α-helix	556-578	23
α-helix	602-613	12
α-helix	626-655	30
α-helix	669-672	4
β-strand	683-684	2	45
α-helix	690-698	9
α-helix	700-706	7
α-helix	707-709	3
α-helix	714-723	10
β-strand	728-732	5	45
α-helix	733-740	8
β-strand	748-750	3	45
β-strand	760-762	3	44
β-strand	765-766	2	42
α-helix	772-785	14
α-helix	788-796	9
β-strand	813	1	35
α-helix	820-842	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	847	Rattus norvegicus	P35439 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	862	Rattus norvegicus	Q00960 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9OBX_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
MSTMHLLTFALLFSCSFARAASDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
QATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRL
ETLLEERESKAEKVLQFDPGTKNVTALLMEARELEARVIILSASEDDAATVYRAAAMLDM
TGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKEN
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFAQYSIMNLQNRK
LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTC
KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMQFTYEVHLVA
DGKFGTQERVQNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI
LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA
LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP
EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQA
VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQQVSLSILKSH
ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH
KDANGAQ

Sequence of entity 2 (B, D), FASTA

>9OBX_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
GWSHPQFEKGGGSGGGSGGSAWSHPQFEKGALVPRGRSQKSPPSIGIAVILVGTSDEVAI
KDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQ
ILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFS
IVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILL
YCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPSEFPTGLISVSYDEWDYGLP
ARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLS
FSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVT
LEEAPFVIVESVDPLSGTCMRNTVPCQKRIISENKTDEEPGYIKKCCKGFCIDILKKISK
SVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFI
ETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLA
DGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANL
AAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFN
QRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDS
GWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMA
LSLITFICEHLFYWQFRHSFMG

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	2
GLU	Glutamic acid	C5 H9 N O4	2

Primary citation

Molecular mechanism of calcium permeability and magnesium block in NMDA receptors. Steigerwald, R., Epstein, M., Chou, T.H. et al. Nat Neurosci (2026) 29:1293-1302. DOI 10.1038/s41593-026-02283-3 · PubMed

Other PDB entries of the same protein (UniProt P35439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1PB7 1.35 Å, Crystal structure of the NR1 ligand binding core in complex with glycine at 1.35 Å…
1Y20 1.4 Å, Crystal structure of the NR1 ligand-binding core in complex with ACPC
1PB8 1.45 Å, Crystal structure of the NR1 ligand binding core in complex with D-serine at 1.45 Å…
1Y1Z 1.5 Å, Crystal structure of the NR1 ligand binding core in complex with ACBC
5U8C 1.6 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…
1PB9 1.6 Å, Crystal structure of the NR1 ligand binding core in complex with D-cycloserine at 1.60 Å…
6UZ6 1.66 Å, Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with…
5I57 1.7 Å, Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains
9NYZ 1.71 Å, Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with…
1Y1M 1.8 Å, Crystal structure of the NR1 ligand binding core in complex with cycloleucine
4NF8 1.86 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and…
6UZR 1.87 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…

Browse structure collections

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