9D3A: Glutamate receptor ionotropic, NMDA 1

Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR (Low-res). Determined by electron microscopy at 3.78 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.78 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,270
Mol. weight: 379.88 kDa
Ligands: GLY, NAG, GLU
Released: 26 Feb 2025

Explore 9D3A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D3A contains 147 α-helices and 146 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: 34 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	1
β-strand	29	1	2
α-helix	36-52	17
β-strand	62	1	2
α-helix	72-81	10
α-helix	83-85	3
β-strand	87	1	1
β-strand	91	1	3
α-helix	105-111	7
α-helix	112-114	3
β-strand	118-120	3	3
α-helix	127-129	3
β-strand	137-139	3	3
α-helix	144-147	4
α-helix	148-157	10
β-strand	164-167	4	4
α-helix	171-185	15
β-strand	194-195	2	4
α-helix	206-210	5
β-strand	218-222	5	4
α-helix	228-237	10
β-strand	246-247	2	4
α-helix	257-260	4
β-strand	268-271	4	5
α-helix	277-296	20
α-helix	318-326	9
β-strand	350-357	8	5
β-strand	360-368	9	5
β-strand	371-374	4	5
α-helix	380-381	2
α-helix	388-390	3
β-strand	400-402	3	6
β-strand	405	1	6
β-strand	409-412	4	6
α-helix	420-422	3
β-strand	424	1	7
α-helix	429	1
β-strand	430	1	7
α-helix	431-432	2
β-strand	434-439	6	6
β-strand	450-457	8	6
α-helix	459-469	11
β-strand	476-478	3	6
β-strand	487-489	3	8
β-strand	496-498	3	8
α-helix	502-505	4
β-strand	512	1	6
β-strand	513	1	9
α-helix	521-524	4
β-strand	528	1	10
β-strand	538-542	5	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	689-695	7
α-helix	697-699	3
α-helix	700-706	7
β-strand	711	1	13
α-helix	714-722	9
β-strand	728-732	5	11
α-helix	733-739	7
β-strand	747-749	3	11
β-strand	761	1	9
β-strand	762	1	10
α-helix	769-775	7
α-helix	785-791	7
α-helix	814-836	23

Chain B: 31 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	35-41	7	14
α-helix	47-52	6
β-strand	66-72	7	14
α-helix	78-91	14
β-strand	94-99	6	14
α-helix	108-118	11
β-strand	123-125	3	14
α-helix	128-131	4
β-strand	143-145	3	14
α-helix	150-163	14
β-strand	168-173	6	15
β-strand	174	1	16
α-helix	179-191	13
β-strand	198-200	3	15
β-strand	205	1	16
α-helix	213-221	9
β-strand	227-231	5	15
α-helix	234-247	14
β-strand	255-258	4	15
α-helix	260-263	4
β-strand	278-282	5	15
α-helix	289-310	22
α-helix	333-337	5
β-strand	351	1	17
β-strand	357	1	17
β-strand	362-366	5	15
β-strand	374-379	6	15
β-strand	384	1	15
β-strand	405-410	6	18
β-strand	413	1	19
β-strand	417	1	19
β-strand	418-420	3	20
α-helix	421-423	3
β-strand	434-436	3	20
β-strand	437	1	18
β-strand	439	1	21
β-strand	452	1	21
β-strand	455-458	4	20
α-helix	460-472	13
β-strand	475-480	6	18
α-helix	497-501	5
β-strand	509	1	18
α-helix	517-520	4
β-strand	524	1	22
β-strand	535-538	4	23
α-helix	556-572	17
α-helix	573-578	6
α-helix	602-611	10
α-helix	612-614	3
α-helix	626-655	30
α-helix	669-672	4
β-strand	683-684	2	23
α-helix	693-698	6
α-helix	700-703	4
α-helix	714-723	10
β-strand	728-731	4	23
α-helix	735-740	6
α-helix	744-746	3
β-strand	749-750	2	23
β-strand	766	1	22
α-helix	767	1
α-helix	773-786	14
α-helix	788-796	9
β-strand	813	1	12
α-helix	820-829	10
α-helix	831-840	10

Chain C: 42 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	24
α-helix	36-39	4
α-helix	40-46	7
α-helix	49-51	3
β-strand	64-66	3	24
α-helix	67-68	2
α-helix	71-74	4
α-helix	75-77	3
α-helix	83-85	3
β-strand	90-92	3	24
α-helix	104-114	11
β-strand	119-120	2	25
β-strand	138-139	2	25
α-helix	144-154	11
β-strand	165-168	4	26
α-helix	171-188	18
β-strand	194-197	4	26
α-helix	206-208	3
α-helix	211-213	3
β-strand	220-221	2	26
α-helix	227-237	11
β-strand	248-249	2	26
α-helix	251-253	3
α-helix	256-259	4
α-helix	277-295	19
α-helix	302-306	5
α-helix	317-326	10
β-strand	330	1	27
β-strand	338	1	27
β-strand	344	1	25
α-helix	388-390	3
β-strand	397	1	28
β-strand	400-402	3	29
β-strand	405	1	30
β-strand	409	1	30
β-strand	412-413	2	31
α-helix	414-415	2
α-helix	416-418	3
α-helix	419-422	4
α-helix	429-432	4
β-strand	434-440	7	31
β-strand	449-455	7	31
β-strand	457	1	30
α-helix	458-469	12
β-strand	473	1	28
β-strand	476-478	3	29
β-strand	487-488	2	32
β-strand	497-498	2	32
α-helix	500-507	8
β-strand	512	1	29
β-strand	513	1	33
α-helix	521-524	4
β-strand	527-528	2	34
β-strand	538-543	6	35
α-helix	544-546	3
α-helix	560-583	24
α-helix	603-615	13
α-helix	627-650	24
α-helix	653-655	3
α-helix	670-673	4
β-strand	681-682	2	36
β-strand	684	1	37
α-helix	688-695	8
α-helix	703-706	4
β-strand	711	1	37
α-helix	714-722	9
β-strand	728-729	2	36
β-strand	730-732	3	35
α-helix	736-742	7
β-strand	746-749	4	35
β-strand	761	1	33
β-strand	762-763	2	34
α-helix	767-769	3
α-helix	774-781	8
α-helix	785-788	4
α-helix	789-793	5
α-helix	815-822	8
α-helix	824-838	15

Chain D: 40 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	54-57	4	38
α-helix	60-62	3
α-helix	69-74	6
α-helix	98-110	13
β-strand	115-118	4	38
α-helix	124-126	3
α-helix	127-137	11
β-strand	141-143	3	38
β-strand	145	1	38
α-helix	147-149	3
α-helix	155-156	2
β-strand	161-163	3	38
α-helix	168-181	14
β-strand	188-189	2	39
α-helix	197-208	12
α-helix	214-215	2
β-strand	219	1	39
α-helix	225-227	3
α-helix	229-235	7
β-strand	243-246	4	39
α-helix	253-263	11
β-strand	271-274	4	39
α-helix	300-301	2
β-strand	304-307	4	39
α-helix	317-335	19
α-helix	344-346	3
β-strand	368	1	40
β-strand	373	1	40
β-strand	376	1	41
β-strand	381	1	38
β-strand	382	1	41
β-strand	388-392	5	39
β-strand	398-403	6	39
β-strand	410-411	2	39
β-strand	431	1	42
β-strand	434-435	2	43
β-strand	436	1	44
β-strand	444-447	4	45
α-helix	448	1
β-strand	449	1	46
β-strand	454	1	46
α-helix	455-456	2
β-strand	460-461	2	45
β-strand	482-485	4	45
α-helix	487-495	9
α-helix	496-500	5
β-strand	502	1	42
β-strand	507	1	44
β-strand	515-516	2	47
β-strand	521-522	2	47
α-helix	524-529	6
β-strand	535-536	2	43
β-strand	561	1	48
β-strand	562-566	5	49
α-helix	574-577	4
α-helix	583-587	5
α-helix	589-604	16
α-helix	629-636	8
α-helix	637-639	3
α-helix	655-682	28
α-helix	686-688	3
α-helix	696-699	4
α-helix	701-703	3
α-helix	707-708	2
β-strand	710-711	2	49
α-helix	717-723	7
α-helix	727-733	7
α-helix	744-750	7
β-strand	755-758	4	49
α-helix	760-766	7
β-strand	775-777	3	49
α-helix	778-780	3
β-strand	784	1	48
β-strand	792	1	43
α-helix	800-812	13
α-helix	815-822	8
α-helix	841-844	4
α-helix	846-871	26

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

>9D3A_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

>9D3A_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

>9D3A_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
GLY	Glycine	C2 H5 N O2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
GLU	Glutamic acid	C5 H9 N O4	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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