9D38: Glutamate receptor ionotropic, NMDA 1

Open state of Gly-,Glu-,EU1622-240 bound GluN1a-2B-2D NMDAR. Determined by electron microscopy at 3.95 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.95 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,024
Mol. weight: 379.66 kDa
Ligands: GLU, NAG, GLY
Released: 26 Feb 2025

Explore 9D38 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D38 contains 135 α-helices and 141 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: 33 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	1
β-strand	31-33	3	2
α-helix	36-52	17
β-strand	59-61	3	1
β-strand	65-66	2	2
α-helix	83-85	3
β-strand	91-92	2	2
α-helix	104-114	11
β-strand	119-120	2	3
α-helix	127-129	3
β-strand	138-139	2	3
α-helix	144-146	3
α-helix	147-156	10
β-strand	164-168	5	4
α-helix	171-181	11
α-helix	184-187	4
β-strand	193-197	5	4
α-helix	205-209	5
α-helix	210-213	4
β-strand	218-222	5	4
α-helix	225-237	13
β-strand	246-249	4	4
α-helix	251-254	4
α-helix	262-263	2
β-strand	266	1	4
β-strand	269-271	3	5
α-helix	277-295	19
α-helix	303-305	3
α-helix	322-324	3
β-strand	341	1	6
β-strand	345	1	6
β-strand	351-357	7	5
β-strand	360-367	8	5
β-strand	372-374	3	5
α-helix	378-379	2
β-strand	400-402	3	7
β-strand	405	1	7
β-strand	409-413	5	7
β-strand	424-425	2	8
β-strand	428-430	3	8
α-helix	431-432	2
β-strand	434-439	6	7
β-strand	450-457	8	7
α-helix	458-467	10
β-strand	476-478	3	7
β-strand	488	1	9
β-strand	497	1	9
α-helix	500-506	7
β-strand	512-513	2	7
α-helix	521-523	3
β-strand	528-529	2	7
β-strand	538-543	6	10
α-helix	544-547	4
α-helix	560-581	22
α-helix	603-614	12
α-helix	627-654	28
α-helix	670-673	4
β-strand	682	1	10
β-strand	684	1	11
α-helix	689-695	7
α-helix	703-706	4
β-strand	711	1	11
α-helix	715-722	8
β-strand	729-732	4	10
α-helix	733-743	11
β-strand	746-749	4	10
β-strand	761-762	2	7
α-helix	769-781	13
α-helix	784-792	9
α-helix	815-836	22

Chain B: 34 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	35-42	8	12
α-helix	48-54	7
β-strand	66-71	6	12
α-helix	78-89	12
β-strand	97-101	5	12
α-helix	108-118	11
β-strand	123-127	5	12
β-strand	143-145	3	12
α-helix	150-164	15
β-strand	168-173	6	13
α-helix	181-191	11
β-strand	198-203	6	13
α-helix	213-219	7
β-strand	227-231	5	13
α-helix	234-247	14
β-strand	255-258	4	13
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	13
α-helix	289-303	15
α-helix	305-310	6
α-helix	325-329	5
α-helix	333-337	5
β-strand	343-344	2	14
β-strand	347-348	2	14
β-strand	362-367	6	13
β-strand	373-375	3	13
β-strand	377-379	3	15
β-strand	384-386	3	15
β-strand	405-410	6	16
β-strand	413	1	16
β-strand	417-421	5	16
α-helix	422-423	2
β-strand	435-439	5	16
β-strand	452-459	8	16
α-helix	461-471	11
β-strand	475-480	6	16
β-strand	489-490	2	17
β-strand	493-494	2	17
α-helix	496-502	7
β-strand	508-509	2	16
α-helix	517-522	6
β-strand	534-536	3	18
β-strand	537-538	2	19
α-helix	539-541	3
α-helix	556-578	23
α-helix	601-613	13
α-helix	630-646	17
α-helix	650-654	5
α-helix	669-672	4
α-helix	674-676	3
α-helix	680-681	2
β-strand	685	1	20
α-helix	691-698	8
α-helix	700-706	7
β-strand	710	1	20
α-helix	714-721	8
β-strand	730-732	3	18
α-helix	733-740	8
α-helix	744-746	3
β-strand	749-750	2	19
β-strand	765-766	2	16
α-helix	772-784	13
α-helix	789-792	4
α-helix	793-795	3
α-helix	819-844	26

Chain C: 32 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	28-32	5	21
α-helix	36-47	12
β-strand	64-65	2	21
α-helix	71-75	5
β-strand	87-93	7	21
α-helix	104-113	10
β-strand	118-121	4	21
β-strand	138-139	2	21
α-helix	144-146	3
α-helix	147-157	11
β-strand	164	1	22
β-strand	165-166	2	23
β-strand	167-168	2	24
α-helix	171-184	14
β-strand	193	1	22
β-strand	196-197	2	24
α-helix	208-211	4
β-strand	220-221	2	23
α-helix	225-234	10
α-helix	257-259	3
α-helix	278-295	18
α-helix	302-306	5
α-helix	317-326	10
β-strand	330	1	25
β-strand	338	1	25
β-strand	354-357	4	26
β-strand	360-363	4	26
β-strand	366-367	2	27
β-strand	371-372	2	27
α-helix	378-380	3
α-helix	382-384	3
β-strand	397-402	6	28
β-strand	405	1	29
β-strand	409-413	5	29
β-strand	424	1	30
β-strand	430	1	30
β-strand	434-436	3	29
β-strand	437	1	28
β-strand	439-440	2	31
β-strand	449-450	2	31
β-strand	453-457	5	29
α-helix	458-468	11
β-strand	473-478	6	28
α-helix	500-507	8
β-strand	512-513	2	28
α-helix	521-524	4
β-strand	538-543	6	32
α-helix	561-582	22
α-helix	604-614	11
α-helix	630-656	27
α-helix	670-673	4
β-strand	681-682	2	33
β-strand	683-684	2	34
α-helix	688-693	6
α-helix	706-708	3
β-strand	710-711	2	34
α-helix	714-722	9
β-strand	728-729	2	33
β-strand	730-732	3	32
α-helix	733-742	10
β-strand	746-749	4	32
β-strand	761-762	2	28
α-helix	771-781	11
α-helix	784-788	5
α-helix	789-793	5
α-helix	813-815	3
α-helix	819-825	7
α-helix	828-835	8
α-helix	836-838	3

Chain D: 36 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	54-56	3	35
α-helix	61-74	14
α-helix	101-105	5
α-helix	106-110	5
β-strand	115-118	4	35
α-helix	124-126	3
α-helix	127-134	8
β-strand	141-145	5	35
β-strand	161-163	3	35
α-helix	168-181	14
β-strand	186	1	36
β-strand	188-189	2	37
α-helix	197-209	13
α-helix	214-215	2
β-strand	216	1	36
α-helix	225-227	3
α-helix	229-234	6
α-helix	235-237	3
β-strand	243-246	4	37
α-helix	250-262	13
β-strand	271-274	4	37
α-helix	300-301	2
β-strand	304-307	4	37
α-helix	317-337	21
α-helix	344-346	3
β-strand	368-369	2	38
β-strand	372-373	2	38
β-strand	376	1	39
β-strand	381	1	35
β-strand	382	1	39
β-strand	386-393	8	37
β-strand	397-405	9	37
β-strand	431-434	4	40
β-strand	443-446	4	40
α-helix	447-449	3
α-helix	455-456	2
β-strand	460-463	4	40
β-strand	481-486	6	40
α-helix	488-499	12
β-strand	502-506	5	40
β-strand	516	1	41
β-strand	521	1	41
α-helix	523-529	7
β-strand	535	1	40
α-helix	546-549	4
β-strand	552	1	42
β-strand	558-566	9	43
β-strand	571	1	44
α-helix	576-578	3
α-helix	582-606	25
α-helix	629-632	4
α-helix	634-638	5
α-helix	653-673	21
α-helix	676-679	4
β-strand	684	1	44
α-helix	696-699	4
α-helix	707-708	2
β-strand	712	1	45
α-helix	718-725	8
α-helix	732-735	4
β-strand	737	1	45
α-helix	742-749	8
β-strand	756-759	4	43
α-helix	762-769	8
β-strand	775-777	3	43
α-helix	778-780	3
β-strand	784-788	5	43
β-strand	792	1	42
α-helix	800-812	13
α-helix	815-823	9
α-helix	847-871	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	825	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B	protein	884	Homo sapiens	Q13224 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2D	D	protein	861	Homo sapiens	O15399 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9D38_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
DPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDL
ISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVP
PYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTK
NVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYA
PDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFK
RVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWP
GGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDT
SPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMM
GELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTL
WLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEG
APRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYA
TVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQ
KCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRS
NAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDANGAQ

Sequence of entity 2 (B), FASTA

>9D38_2 Glutamate receptor ionotropic, NMDA 2B (chains B)
WSHPQFEKGGGSGGGSGGSAWSHPQFEKGALVPRGRSQKSPPSIGIAVILVGTSDEVAIK
DAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQI
LDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSI
VTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLY
CTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPA
RVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSF
SEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTL
EEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKS
VKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIE
TGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRSLAD
GREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLA
AFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQ
RGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSG
WKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMAL
SLITFISEHLFYWQFRHSFMGGPGSGATNFSLLKQAGDVEENPG

Sequence of entity 3 (D), FASTA

>9D38_3 Glutamate receptor ionotropic, NMDA 2D (chains D)
FPEEAPGPGGAGGPGGGLGGARPLNVALVFSGPAYAAEAARLGPAVAAAVRSPGLDVRPV
ALVLNGSDPRSLVLQLCDLLSGLRVHGVVFEDDSRAPAVAPILDFLSAQTSLPIVAVHGG
AALVLTPKEKGSTFLQLGSSTEQQLQVIFEVLEEYDWTSFVAVTTRAPGHRAFLSYIEVL
TDGSLVGWEHRGALTLDPGAGEAVLSAQLRSVSAQIRLLFCAREEAEPVFRAAEEAGLTG
SGYVWFMVGPQLAGGGGSGAPGEPPLLPGGAPLPAGLFAVRSAGWRDDLARRVAAGVAVV
ARGAQALLRDYGFLPELGHDCRAQNRTHRGESLHRYFMNITWDNRDYSFNEDGFLVNPSL
VVISLTRDRTWEVVGSWEQQTLRLKYPLWSRYGRFLQPVDDTQHLTVATLEERPFVIVEP
ADPISGTCIRDSVPCRSQLNRTHSPPPDAPRPEKRCCKGFCIDILKRLAHTIGFSYDLYL
VTNGKHGKKIDGVWNGMIGEVFYQRADMAIGSLTINEERSEIVDFSVPFVETGISVMVAR
SNGTVSPSAFLEPYSPAVWVMMFVMCLTVVAVTVFIFEYLSPVGYNRSLATGKRPGGSTF
TIGKSIWLLWALVFNNSVPVENPRGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYV
DTVSGLSDRKFQRPQEQYPPLKFGTVPNGSTEKNIRSNYPDMHSYMVRYNQPRVEEALTQ
LKAGKLDAFIYDAAVLNYMARKDEGCKLVTIGSGKVFATTGYGIALHKGSRWKRPIDLAL
LQFLGDDEIEMLERLWLSGICHNDKIEVMSSKLDIDNMAGVFYMLLVAMGLSLLVFAWEH
LVYWRLRHCLGPTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
GLU	Glutamic acid	C5 H9 N O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
GLY	Glycine	C2 H5 N O2	2

Primary citation

Structural basis for channel gating and blockade in tri-heteromeric GluN1-2B-2D NMDA receptor. Kang, H., Epstein, M., Banke, T.G. et al. Neuron (2025) 113:991. DOI 10.1016/j.neuron.2025.01.013 · PubMed

Other PDB entries of the same protein (UniProt Q05586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GJ1 1.62 Å, NMDA bound to compound 339
5H8F 1.81 Å, Structure of the apo human GluN1/GluN2A LBD
9GIC 1.82 Å, NMDA bound to compound 345
3BYA 1.85 Å, Structure of a Calmodulin Complex
5H8Q 1.9 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE8324
9GIF 1.9 Å, NMDA bound to compound 288
9GIB 1.95 Å, NMDA bound to compound 380
9MUM 1.97 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11,…
9GID 2.0 Å, NMDA bound to compound 338
5KCJ 2.09 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE6901
9GIG 2.09 Å, NMDA bound to compound 387
5I2N 2.12 Å, Structure of the human GluN1/GluN2A LBD in complex with…

Browse structure collections

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