9D39: Gly-,PPDA- bound GluN1a-2B-2D NMDAR

Gly-,PPDA- bound GluN1a-2B-2D NMDAR. Determined by electron microscopy at 3.65 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.65 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,275
Mol. weight: 379.7 kDa
Ligands: GLY, NAG, 2JL
Released: 26 Feb 2025

Explore 9D39 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D39 contains 136 α-helices and 145 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: 38 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	1
α-helix	36-50	15
β-strand	59-64	6	1
α-helix	73-76	4
α-helix	83-85	3
β-strand	87-89	3	1
β-strand	90-91	2	2
α-helix	104-110	7
β-strand	118-120	3	2
β-strand	138-139	2	2
α-helix	144-146	3
α-helix	147-156	10
β-strand	163-168	6	3
α-helix	171-185	15
β-strand	194-197	4	3
α-helix	204-207	4
α-helix	208-213	6
β-strand	218-222	5	3
α-helix	228-237	10
β-strand	246-249	4	3
α-helix	251-254	4
α-helix	263	1
β-strand	270-271	2	4
α-helix	277-295	19
α-helix	304-306	3
α-helix	320-323	4
α-helix	325-327	3
β-strand	339-340	2	5
β-strand	345	1	2
β-strand	346-347	2	5
β-strand	351-353	3	4
β-strand	356-357	2	6
β-strand	360-361	2	6
β-strand	365-367	3	4
β-strand	372-374	3	4
α-helix	378-379	2
α-helix	388-389	2
β-strand	397-402	6	7
β-strand	410-413	4	7
α-helix	414-415	2
α-helix	420-422	3
β-strand	424	1	8
α-helix	429	1
β-strand	430	1	8
α-helix	431-432	2
β-strand	433-437	5	7
β-strand	452-456	5	7
α-helix	458-468	11
β-strand	473-478	6	7
β-strand	485-488	4	9
β-strand	497-500	4	9
α-helix	501-506	6
β-strand	512-513	2	7
β-strand	515	1	10
α-helix	523-525	3
β-strand	528	1	7
β-strand	538-543	6	11
α-helix	544-547	4
α-helix	560-582	23
α-helix	605-615	11
α-helix	627-656	30
α-helix	670-673	4
β-strand	682	1	11
β-strand	684	1	12
α-helix	689-695	7
α-helix	700-706	7
α-helix	710	1
β-strand	711	1	12
α-helix	714-722	9
β-strand	729-732	4	11
α-helix	733-742	10
β-strand	746-748	3	11
β-strand	759	1	10
β-strand	762	1	7
α-helix	769-781	13
α-helix	785-792	8
α-helix	814-836	23

Chain B: 31 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	38-41	4	13
α-helix	47-55	9
α-helix	78-92	15
β-strand	97-100	4	13
α-helix	108-118	11
β-strand	123-127	5	13
α-helix	133-134	2
β-strand	143-144	2	13
α-helix	150-164	15
β-strand	168-173	6	14
α-helix	179-190	12
β-strand	198-204	7	14
α-helix	213-220	8
β-strand	227-230	4	14
α-helix	234-247	14
β-strand	255-258	4	14
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	14
α-helix	289-311	23
α-helix	324-327	4
α-helix	333-339	7
β-strand	343-344	2	15
β-strand	347-348	2	15
α-helix	350	1
β-strand	351	1	16
α-helix	352	1
β-strand	357	1	16
β-strand	362-367	6	14
β-strand	373-380	8	14
β-strand	383-386	4	14
β-strand	405-406	2	17
β-strand	409	1	18
β-strand	418	1	19
β-strand	434-436	3	20
β-strand	437-438	2	21
β-strand	455-457	3	20
β-strand	458	1	19
α-helix	460-472	13
β-strand	475-476	2	17
β-strand	479-480	2	21
β-strand	490	1	22
β-strand	493	1	22
α-helix	496-502	7
β-strand	508-514	7	18
α-helix	515	1
β-strand	524	1	18
β-strand	534-537	4	23
β-strand	538-539	2	24
α-helix	556-575	20
α-helix	602-613	12
α-helix	626-653	28
α-helix	669-672	4
α-helix	679-681	3
β-strand	683-684	2	23
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	23
α-helix	733-741	9
β-strand	748-749	2	24
β-strand	762-766	5	18
α-helix	772-785	14
α-helix	789-796	8
α-helix	820-837	18

Chain C: 35 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	28-32	5	25
α-helix	36-43	8
α-helix	66-68	3
α-helix	72-75	4
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	25
α-helix	104-114	11
β-strand	118-120	3	25
β-strand	138-139	2	25
α-helix	144-146	3
α-helix	147-156	10
β-strand	164	1	26
β-strand	165-166	2	27
β-strand	167-168	2	28
α-helix	171-181	11
β-strand	193	1	26
β-strand	196-197	2	28
α-helix	206-209	4
β-strand	220-221	2	27
α-helix	225-234	10
β-strand	247	1	29
β-strand	248-249	2	27
α-helix	256-258	3
β-strand	266	1	29
α-helix	278-295	18
α-helix	302-306	5
α-helix	318-327	10
β-strand	330	1	30
β-strand	338	1	30
β-strand	344	1	25
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	388-390	3
β-strand	397-402	6	33
β-strand	405	1	34
β-strand	409	1	34
β-strand	410-413	4	35
α-helix	416-418	3
α-helix	420-422	3
β-strand	424	1	36
β-strand	430	1	36
β-strand	434-439	6	35
β-strand	450-456	7	35
α-helix	458-470	13
β-strand	473-478	6	33
β-strand	488-489	2	37
β-strand	496-497	2	37
α-helix	500-507	8
β-strand	512-513	2	33
α-helix	521-524	4
β-strand	527-528	2	33
β-strand	538-543	6	38
α-helix	563-579	17
α-helix	603-614	12
α-helix	629-657	29
α-helix	666-668	3
α-helix	670-673	4
β-strand	684	1	39
α-helix	688-692	5
α-helix	697-699	3
α-helix	700-706	7
β-strand	711	1	39
α-helix	714-722	9
β-strand	730-732	3	38
α-helix	733-742	10
β-strand	746-749	4	38
β-strand	761-763	3	33
α-helix	768-782	15
α-helix	784-791	8
α-helix	806-808	3
α-helix	810-835	26

Chain D: 32 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	53-58	6	40
α-helix	60-62	3
α-helix	65-74	10
β-strand	86-87	2	40
α-helix	98-105	8
α-helix	106-110	5
β-strand	115-119	5	40
α-helix	126-137	12
β-strand	141-145	5	40
α-helix	155-156	2
β-strand	161	1	40
β-strand	166	1	41
α-helix	168-181	14
β-strand	188-191	4	42
β-strand	192	1	43
α-helix	197-207	11
β-strand	223	1	43
α-helix	229-236	8
β-strand	243-247	5	42
α-helix	250-262	13
β-strand	271-274	4	42
β-strand	305-306	2	42
α-helix	317-337	21
β-strand	368-369	2	44
β-strand	372-373	2	44
β-strand	376	1	41
β-strand	382	1	41
β-strand	387-392	6	42
β-strand	398-404	7	42
β-strand	431-436	6	45
β-strand	439	1	46
β-strand	443-446	4	46
α-helix	455-456	2
β-strand	460	1	46
β-strand	463-464	2	45
β-strand	483-486	4	46
α-helix	487-495	9
α-helix	496-500	5
β-strand	502-507	6	45
β-strand	515-516	2	47
β-strand	521-522	2	47
α-helix	523-529	7
β-strand	535	1	45
α-helix	544-547	4
β-strand	564-566	3	48
α-helix	567-568	2
α-helix	583-605	23
α-helix	628-640	13
α-helix	653-680	28
α-helix	696-699	4
α-helix	707-709	3
β-strand	710-711	2	49
α-helix	717-725	9
α-helix	727-733	7
α-helix	734-736	3
α-helix	741-749	9
β-strand	755-756	2	49
α-helix	760-768	9
α-helix	771-773	3
β-strand	775-777	3	48
α-helix	800-812	13
α-helix	815-821	7
α-helix	843-845	3
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

>9D39_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

>9D39_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

>9D39_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	3
2JL	(2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid	C21 H18 N2 O5	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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