9D3C: Glutamate receptor ionotropic, NMDA 1

Gly-,Glu-,(S)-(+)-ketamine bound GluN1a-2B-2D NMDAR. Determined by electron microscopy at 3.96 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.96 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,194
Mol. weight: 381 kDa
Ligands: JC9, GLU, NAG, GLY
Released: 26 Feb 2025

Explore 9D3C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D3C contains 138 α-helices and 157 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: 36 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	1
α-helix	40-52	13
β-strand	61-66	6	1
α-helix	74-79	6
α-helix	83-85	3
β-strand	87	1	1
β-strand	90-91	2	2
β-strand	92	1	1
α-helix	106-113	8
β-strand	118-120	3	2
β-strand	138-139	2	2
α-helix	144-147	4
α-helix	148-157	10
β-strand	164-168	5	3
α-helix	171-184	14
β-strand	194-197	4	3
α-helix	205-208	4
α-helix	209-213	5
β-strand	218-222	5	3
α-helix	225-237	13
β-strand	246-249	4	3
α-helix	252-254	3
α-helix	259-261	3
α-helix	262-263	2
β-strand	267-271	5	3
α-helix	277-295	19
α-helix	302-305	4
α-helix	318-326	9
β-strand	340	1	4
β-strand	346	1	4
β-strand	351-357	7	3
β-strand	360-367	8	3
β-strand	372-374	3	3
α-helix	382-384	3
α-helix	388-389	2
β-strand	397-402	6	5
β-strand	405	1	5
β-strand	409-413	5	5
α-helix	419-421	3
α-helix	430-432	3
β-strand	434-437	4	5
β-strand	453-457	5	5
α-helix	460-466	7
β-strand	473-478	6	5
β-strand	487-490	4	6
β-strand	495-498	4	6
α-helix	500-506	7
β-strand	512-513	2	5
α-helix	521-524	4
β-strand	528	1	7
β-strand	538-542	5	8
α-helix	560-579	20
α-helix	603-615	13
α-helix	627-656	30
α-helix	670-673	4
β-strand	681-682	2	9
β-strand	684	1	10
α-helix	689-695	7
α-helix	701-706	6
β-strand	711	1	10
α-helix	716-721	6
β-strand	728-729	2	9
β-strand	730-732	3	8
α-helix	733-743	11
β-strand	747-749	3	8
β-strand	761	1	5
β-strand	762	1	7
α-helix	769-780	12
α-helix	784-789	6
α-helix	790-794	5
α-helix	819-826	8
α-helix	828-840	13

Chain B: 28 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	38-42	5	11
α-helix	50-56	7
β-strand	70-73	4	11
α-helix	78-91	14
β-strand	97-101	5	11
α-helix	108-118	11
β-strand	123-125	3	11
α-helix	128-130	3
β-strand	143-144	2	11
α-helix	150-158	9
β-strand	168-171	4	12
β-strand	172-173	2	13
α-helix	180-190	11
β-strand	198-199	2	12
β-strand	203-204	2	13
α-helix	215-219	5
β-strand	227-229	3	12
α-helix	234-247	14
β-strand	255-258	4	12
α-helix	273-274	2
β-strand	278-282	5	12
α-helix	289-310	22
α-helix	335-338	4
β-strand	344	1	14
β-strand	347	1	14
β-strand	362-367	6	12
β-strand	373-380	8	12
β-strand	383-386	4	12
α-helix	391-393	3
β-strand	405	1	15
β-strand	408-410	3	16
β-strand	413	1	17
β-strand	417	1	17
β-strand	418-420	3	16
α-helix	421-423	3
β-strand	434-437	4	16
β-strand	439	1	18
β-strand	452	1	18
β-strand	455-458	4	16
α-helix	460-472	13
β-strand	475	1	15
β-strand	478-480	3	16
β-strand	490	1	19
β-strand	493	1	19
α-helix	496-502	7
β-strand	508-509	2	16
α-helix	518-521	4
β-strand	524	1	16
β-strand	531-532	2	20
β-strand	534-539	6	21
α-helix	556-576	21
α-helix	602-613	12
α-helix	626-654	29
α-helix	669-672	4
β-strand	684	1	21
α-helix	691-698	8
α-helix	700-705	6
α-helix	706-709	4
α-helix	714-722	9
β-strand	729-732	4	21
α-helix	733-741	9
β-strand	748-750	3	21
β-strand	760-761	2	20
β-strand	765-766	2	16
α-helix	773-785	13
α-helix	789-796	8
α-helix	819-844	26

Chain C: 36 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	22
α-helix	38-53	16
β-strand	61	1	22
β-strand	64-66	3	22
α-helix	73-75	3
α-helix	77-80	4
α-helix	83-85	3
β-strand	87-93	7	22
α-helix	104-113	10
β-strand	118-121	4	22
β-strand	138-139	2	22
α-helix	144-147	4
α-helix	148-157	10
β-strand	164-166	3	23
β-strand	167-168	2	24
α-helix	171-182	12
β-strand	193	1	23
β-strand	196-197	2	24
α-helix	206-210	5
β-strand	218-221	4	23
α-helix	225-236	12
β-strand	246-249	4	23
α-helix	251-253	3
α-helix	256-258	3
β-strand	266-268	3	23
α-helix	278-290	13
α-helix	291-295	5
α-helix	302-305	4
α-helix	318-325	8
β-strand	354-357	4	23
β-strand	360-363	4	23
β-strand	367	1	25
β-strand	371	1	25
β-strand	398-400	3	26
β-strand	401	1	27
β-strand	405	1	26
β-strand	409-412	4	26
β-strand	424	1	28
α-helix	429	1
β-strand	430	1	28
α-helix	431	1
β-strand	434-437	4	26
β-strand	439	1	29
β-strand	450	1	29
β-strand	453-457	5	26
α-helix	459-470	12
β-strand	474-477	4	26
β-strand	487	1	30
β-strand	498	1	30
α-helix	501-507	7
β-strand	512-513	2	27
α-helix	523-525	3
β-strand	527-528	2	27
β-strand	535-536	2	31
β-strand	538-543	6	32
α-helix	546-548	3
α-helix	560-582	23
α-helix	603-615	13
α-helix	629-651	23
α-helix	653-655	3
α-helix	657-660	4
α-helix	670-673	4
β-strand	681-682	2	32
β-strand	684	1	33
α-helix	688-693	6
α-helix	703-706	4
α-helix	707-709	3
β-strand	711	1	33
α-helix	714-722	9
β-strand	728-732	5	32
α-helix	733-739	7
β-strand	746-749	4	32
β-strand	756-757	2	31
β-strand	761-763	3	27
α-helix	775-782	8
α-helix	784-790	7
α-helix	816-837	22

Chain D: 38 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	54-57	4	34
β-strand	58	1	35
α-helix	60-62	3
α-helix	63-76	14
β-strand	88	1	34
β-strand	91	1	35
α-helix	96-109	14
β-strand	115-118	4	34
α-helix	126-135	10
β-strand	141-143	3	34
α-helix	147-149	3
α-helix	155-156	2
β-strand	161-162	2	34
α-helix	168-182	15
β-strand	186	1	36
β-strand	188-191	4	37
α-helix	199-203	5
α-helix	204-207	4
β-strand	216	1	36
α-helix	232-234	3
β-strand	244-247	4	37
α-helix	253-261	9
β-strand	272-274	3	37
β-strand	304-305	2	37
β-strand	306-307	2	38
α-helix	319-337	19
α-helix	344-346	3
β-strand	368-369	2	39
β-strand	372-373	2	39
β-strand	376	1	40
β-strand	382	1	40
β-strand	389-390	2	38
β-strand	391-393	3	41
β-strand	397-399	3	41
β-strand	431-433	3	42
β-strand	436	1	43
β-strand	439	1	44
β-strand	443	1	44
β-strand	444-446	3	45
α-helix	447-449	3
α-helix	455-456	2
β-strand	460-462	3	45
β-strand	482-485	4	45
α-helix	487-495	9
α-helix	496-500	5
β-strand	502-504	3	42
β-strand	507	1	43
β-strand	517	1	46
β-strand	520	1	46
α-helix	523-528	6
β-strand	536	1	47
α-helix	544-547	4
β-strand	552	1	47
β-strand	558-561	4	48
β-strand	562-563	2	49
β-strand	564-566	3	50
α-helix	567-568	2
α-helix	585-606	22
α-helix	629-638	10
α-helix	653-680	28
α-helix	696-699	4
α-helix	707-708	2
α-helix	717-720	4
α-helix	722-724	3
α-helix	727-733	7
α-helix	734-736	3
α-helix	742-750	9
β-strand	757-758	2	49
α-helix	761-766	6
α-helix	771-773	3
β-strand	775-777	3	50
α-helix	778-781	4
β-strand	784-788	5	48
β-strand	792	1	47
α-helix	800-812	13
α-helix	815-823	9
α-helix	843-845	3
α-helix	849-863	15
α-helix	866-869	4

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

>9D3C_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

>9D3C_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

>9D3C_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
JC9	(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one	C13 H16 Cl N O	1
GLU	Glutamic acid	C5 H9 N O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8
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

About this viewer

MolViewer shows 9D3C directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.