9D37: Glutamate receptor ionotropic, NMDA 1

Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR. Determined by electron microscopy at 3.34 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.34 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,274
Mol. weight: 379.88 kDa
Ligands: GLU, NAG, GLY
Released: 26 Feb 2025

Explore 9D37 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D37 contains 142 α-helices and 150 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, 38 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	1
β-strand	31	1	2
α-helix	36-52	17
α-helix	72-81	10
α-helix	83-85	3
β-strand	87	1	1
β-strand	90-92	3	2
α-helix	107-110	4
β-strand	118-120	3	2
α-helix	127-129	3
β-strand	137-139	3	2
α-helix	144-147	4
α-helix	148-157	10
β-strand	163-168	6	3
α-helix	171-185	15
β-strand	193-197	5	3
α-helix	206-212	7
β-strand	218-222	5	3
α-helix	228-237	10
β-strand	246-247	2	3
α-helix	251-254	4
α-helix	257-261	5
β-strand	267-271	5	4
α-helix	277-296	20
α-helix	318-325	8
β-strand	340	1	5
β-strand	346	1	5
β-strand	350-357	8	4
β-strand	360-368	9	4
β-strand	371-374	4	4
α-helix	382-384	3
α-helix	388-390	3
β-strand	397-402	6	6
β-strand	405	1	7
β-strand	409	1	7
β-strand	410-413	4	8
α-helix	414-415	2
α-helix	420-421	2
β-strand	424	1	9
α-helix	429	1
β-strand	430	1	9
α-helix	431	1
β-strand	434-439	6	8
β-strand	450-456	7	8
α-helix	458-470	13
β-strand	473-478	6	6
β-strand	486-489	4	10
β-strand	496-499	4	10
α-helix	501-505	5
β-strand	512-513	2	6
α-helix	523-525	3
β-strand	528	1	11
β-strand	538-541	4	12
β-strand	558	1	13
α-helix	560-582	23
α-helix	603-615	13
α-helix	627-654	28
α-helix	670-673	4
β-strand	681-682	2	12
β-strand	684	1	14
α-helix	689-695	7
α-helix	700-706	7
β-strand	711	1	14
α-helix	714-722	9
β-strand	728-732	5	12
α-helix	733-743	11
β-strand	748-749	2	12
β-strand	761	1	6
β-strand	762	1	11
α-helix	769-781	13
α-helix	784-792	9
α-helix	815-836	22

Chain B: 32 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	36-41	6	15
α-helix	47-52	6
β-strand	68-72	5	15
α-helix	78-91	14
β-strand	94-99	6	15
α-helix	108-118	11
β-strand	123-125	3	15
α-helix	128-131	4
β-strand	143-145	3	15
α-helix	150-164	15
β-strand	168-173	6	16
α-helix	179-191	13
β-strand	198-199	2	16
α-helix	213-220	8
β-strand	227-231	5	16
α-helix	234-247	14
β-strand	255-258	4	16
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	16
α-helix	289-310	22
α-helix	333-338	6
α-helix	350	1
β-strand	351	1	17
α-helix	352	1
β-strand	357	1	17
β-strand	362-366	5	16
β-strand	374-375	2	16
β-strand	379	1	16
β-strand	384	1	16
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	460-471	12
β-strand	475-480	6	18
β-strand	488-490	3	22
β-strand	493-495	3	22
α-helix	497-501	5
β-strand	509	1	18
α-helix	517-520	4
β-strand	524-525	2	23
β-strand	535-538	4	24
α-helix	560-572	13
α-helix	573-577	5
α-helix	602-613	12
α-helix	626-653	28
α-helix	669-672	4
β-strand	683-684	2	24
α-helix	690-698	9
α-helix	700-705	6
α-helix	714-723	10
β-strand	728-731	4	24
α-helix	733-741	9
α-helix	744-746	3
β-strand	749-750	2	24
β-strand	765-766	2	23
α-helix	767	1
α-helix	773-786	14
α-helix	788-796	9
β-strand	813	1	13
α-helix	820-839	20

Chain C: 39 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	25
β-strand	31-33	3	26
α-helix	36-39	4
α-helix	40-47	8
β-strand	61	1	25
β-strand	64-66	3	26
α-helix	67-68	2
α-helix	72-77	6
α-helix	83-85	3
β-strand	92	1	26
α-helix	104-113	10
α-helix	126-128	3
β-strand	138	1	27
α-helix	144-146	3
α-helix	147-156	10
β-strand	164-168	5	28
α-helix	171-188	18
β-strand	193-197	5	28
α-helix	206-209	4
α-helix	211-213	3
β-strand	220-222	3	28
α-helix	227-236	10
β-strand	247	1	29
β-strand	248-249	2	28
α-helix	251-253	3
α-helix	256-258	3
β-strand	266	1	29
α-helix	277-295	19
α-helix	302-305	4
α-helix	318-326	9
β-strand	330	1	30
β-strand	338	1	30
β-strand	344	1	27
β-strand	354-356	3	31
β-strand	361-363	3	31
β-strand	366-367	2	32
β-strand	371-372	2	32
α-helix	388-389	2
β-strand	397	1	33
β-strand	400-402	3	34
β-strand	405	1	35
β-strand	409	1	35
β-strand	410-412	3	34
α-helix	416-418	3
β-strand	424	1	36
α-helix	429	1
β-strand	430	1	36
α-helix	431	1
β-strand	434-439	6	34
β-strand	450-456	7	34
α-helix	458-470	13
β-strand	473	1	33
β-strand	476-478	3	34
β-strand	488-489	2	37
β-strand	496-497	2	37
α-helix	501-505	5
β-strand	512-513	2	34
α-helix	521-524	4
β-strand	527-528	2	34
β-strand	538-543	6	38
α-helix	544-546	3
α-helix	560-583	24
α-helix	603-615	13
α-helix	627-651	25
α-helix	670-673	4
β-strand	681-682	2	38
β-strand	684	1	39
α-helix	688-692	5
α-helix	703-706	4
β-strand	711	1	39
α-helix	714-722	9
β-strand	728-732	5	38
α-helix	733-742	10
β-strand	746-749	4	38
β-strand	761-763	3	34
α-helix	767-769	3
α-helix	771-781	11
α-helix	785-792	8
α-helix	815-821	7
α-helix	826-838	13

Chain D: 37 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	54-57	4	40
α-helix	60-62	3
α-helix	63-74	12
α-helix	98-110	13
β-strand	115-118	4	40
α-helix	124-126	3
α-helix	127-136	10
β-strand	141-145	5	40
α-helix	147-149	3
α-helix	155-156	2
β-strand	162-163	2	40
α-helix	168-181	14
β-strand	188-191	4	41
α-helix	197-202	6
α-helix	204-207	4
α-helix	229-235	7
β-strand	243-247	5	41
α-helix	250-263	14
β-strand	271-274	4	41
α-helix	300-301	2
β-strand	304-307	4	41
α-helix	317-337	21
α-helix	344-346	3
β-strand	368	1	42
β-strand	373	1	42
β-strand	376	1	43
β-strand	382	1	43
β-strand	389-392	4	41
β-strand	398-400	3	41
β-strand	431	1	44
β-strand	434-436	3	45
β-strand	439	1	46
β-strand	443	1	46
β-strand	444-447	4	47
α-helix	448-449	2
α-helix	455-456	2
β-strand	460-462	3	47
β-strand	463-464	2	45
β-strand	482-485	4	47
α-helix	487-495	9
α-helix	496-500	5
β-strand	502	1	44
β-strand	505-507	3	45
β-strand	515-516	2	48
β-strand	521-522	2	48
α-helix	524-529	6
β-strand	535-536	2	45
β-strand	541	1	49
α-helix	546-548	3
β-strand	561-566	6	50
α-helix	574-577	4
α-helix	583-587	5
α-helix	589-602	14
α-helix	603-605	3
α-helix	630-640	11
α-helix	655-682	28
α-helix	686-688	3
α-helix	696-699	4
α-helix	701-703	3
β-strand	710-711	2	50
α-helix	717-723	7
α-helix	727-732	6
α-helix	741-750	10
β-strand	755-759	5	50
α-helix	760-768	9
β-strand	775-777	3	50
β-strand	784	1	50
β-strand	789	1	49
β-strand	792	1	45
α-helix	800-812	13
α-helix	815-823	9
α-helix	841-871	31

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

>9D37_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

>9D37_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

>9D37_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	4
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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