4PE5: GluN1a/GluN2B NMDA Receptor Ion Channel

Crystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel. Determined by X-ray diffraction at 3.96 Å resolution. Released 4 Jun 2014.

Method: X-ray diffraction
Resolution: 3.96 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 20,246
Mol. weight: 392.81 kDa
Ligands: NAG, GLY, W, GLU
Released: 4 Jun 2014

Explore 4PE5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PE5 contains 131 α-helices and 160 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, 41 β-strands

Element	Residues	Length	Sheet
β-strand	26-33	8	1
α-helix	36-51	16
β-strand	59-66	8	1
α-helix	67-68	2
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	1
α-helix	105-113	9
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-146	3
α-helix	147-158	12
β-strand	162-168	7	2
α-helix	171-184	14
β-strand	190-197	8	2
α-helix	205-212	8
β-strand	218-222	5	2
α-helix	225-237	13
β-strand	246-248	3	2
α-helix	252-254	3
α-helix	257-260	4
α-helix	262-263	2
β-strand	267-271	5	2
α-helix	277-295	19
α-helix	301-305	5
α-helix	318-326	9
β-strand	330-333	4	3
β-strand	336-338	3	3
β-strand	339-340	2	4
β-strand	345	1	1
β-strand	346-347	2	4
β-strand	351-357	7	2
β-strand	360-367	8	2
β-strand	372-374	3	2
α-helix	378-379	2
α-helix	388-389	2
β-strand	397-398	2	5
β-strand	400-402	3	6
β-strand	405	1	6
β-strand	409-412	4	6
β-strand	424	1	7
β-strand	430	1	7
β-strand	434-438	5	6
β-strand	451-457	7	6
α-helix	458-469	12
β-strand	473-474	2	5
β-strand	477-478	2	6
β-strand	485-489	5	8
β-strand	496-500	5	8
α-helix	501-505	5
β-strand	512-518	7	6
α-helix	521-524	4
β-strand	528	1	6
β-strand	534	1	6
β-strand	538-543	6	9
α-helix	544-547	4
α-helix	559-581	23
α-helix	606-614	9
α-helix	630-653	24
α-helix	670-673	4
β-strand	681-682	2	9
β-strand	684	1	10
α-helix	688-694	7
α-helix	697-699	3
α-helix	700-706	7
β-strand	711	1	10
α-helix	714-722	9
β-strand	728-732	5	9
α-helix	733-739	7
β-strand	746-748	3	9
β-strand	753	1	9
β-strand	758-762	5	6
α-helix	767-781	15
α-helix	784-790	7
α-helix	810-829	20

Chain B: 29 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	11
α-helix	47-52	6
β-strand	65-73	9	11
α-helix	78-91	14
β-strand	94-100	7	11
α-helix	106-118	13
β-strand	123-127	5	11
α-helix	128-131	4
β-strand	143-145	3	11
α-helix	150-163	14
β-strand	168-174	7	12
α-helix	179-191	13
β-strand	198-205	8	12
α-helix	215-221	7
β-strand	227-231	5	12
α-helix	234-247	14
β-strand	255-258	4	12
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	12
α-helix	289-308	20
α-helix	315-318	4
α-helix	336-339	4
β-strand	343-344	2	13
β-strand	347-348	2	13
β-strand	351	1	14
β-strand	357	1	14
β-strand	362-367	6	12
β-strand	373-380	8	12
β-strand	383-386	4	12
β-strand	405-410	6	15
β-strand	413	1	16
β-strand	417	1	16
β-strand	418-420	3	15
α-helix	421-423	3
β-strand	434-438	5	15
β-strand	453-458	6	15
α-helix	460-471	12
β-strand	475-480	6	15
β-strand	489	1	17
β-strand	494	1	17
α-helix	497-502	6
β-strand	508-510	3	15
β-strand	514	1	18
α-helix	519-522	4
β-strand	524-525	2	15
α-helix	526-528	3
β-strand	531-536	6	19
β-strand	537-538	2	20
α-helix	556-568	13
α-helix	604-611	8
α-helix	632-656	25
α-helix	669-672	4
β-strand	683-684	2	21
α-helix	690-695	6
α-helix	700-705	6
α-helix	714-723	10
β-strand	728-729	2	21
β-strand	730-732	3	19
α-helix	733-741	9
β-strand	749-750	2	20
β-strand	757-761	5	19
β-strand	762	1	18
β-strand	765-766	2	15
α-helix	773-786	14
α-helix	788-795	8
α-helix	822-839	18

Chain C: 36 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	26-33	8	22
α-helix	36-52	17
β-strand	59-66	8	22
α-helix	67-68	2
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	22
α-helix	105-113	9
β-strand	118-120	3	22
α-helix	126-129	4
β-strand	137-139	3	22
α-helix	144-146	3
α-helix	147-157	11
β-strand	162-168	7	23
α-helix	171-184	14
β-strand	190-197	8	23
α-helix	205-212	8
β-strand	218-222	5	23
α-helix	225-237	13
β-strand	246-248	3	23
α-helix	252-254	3
α-helix	257-260	4
α-helix	262-263	2
β-strand	267-271	5	23
α-helix	277-295	19
α-helix	301-305	5
α-helix	318-326	9
β-strand	330-333	4	24
β-strand	336-338	3	24
β-strand	339-340	2	25
β-strand	345	1	22
β-strand	346-347	2	25
β-strand	351-357	7	23
β-strand	360-367	8	23
β-strand	372-374	3	23
α-helix	378-379	2
α-helix	388-389	2
β-strand	397-398	2	26
β-strand	400-402	3	27
β-strand	405	1	27
β-strand	409-412	4	27
α-helix	413-414	2
β-strand	424	1	28
β-strand	430	1	28
β-strand	434-439	6	27
β-strand	450-457	8	27
α-helix	458-469	12
β-strand	473-474	2	26
β-strand	477-478	2	27
β-strand	485-489	5	29
β-strand	496-500	5	29
α-helix	501-506	6
β-strand	512-513	2	27
β-strand	518	1	30
α-helix	521-524	4
β-strand	528-529	2	27
β-strand	534	1	30
β-strand	538-543	6	31
α-helix	559-580	22
α-helix	606-614	9
α-helix	635-656	22
α-helix	660-661	2
α-helix	670-673	4
β-strand	681-682	2	31
β-strand	684	1	32
α-helix	688-694	7
α-helix	700-706	7
β-strand	711	1	32
α-helix	714-722	9
β-strand	728-732	5	31
α-helix	733-739	7
β-strand	746-748	3	31
β-strand	753	1	31
β-strand	758	1	30
β-strand	761-762	2	27
α-helix	767-781	15
α-helix	784-790	7
α-helix	810-830	21

Chain D: 30 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	33
α-helix	47-55	9
β-strand	65-73	9	33
α-helix	78-91	14
β-strand	94-100	7	33
α-helix	106-119	14
β-strand	123-127	5	33
α-helix	128-131	4
β-strand	143-145	3	33
α-helix	150-163	14
β-strand	168-174	7	34
α-helix	179-191	13
β-strand	198-205	8	34
α-helix	215-220	6
β-strand	227-231	5	34
α-helix	234-245	12
β-strand	255-258	4	34
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	34
α-helix	289-311	23
α-helix	327-330	4
α-helix	336-339	4
β-strand	343-344	2	35
β-strand	347-348	2	35
β-strand	351	1	36
β-strand	357	1	36
β-strand	361-367	7	34
β-strand	373-380	8	34
β-strand	383-386	4	34
β-strand	405-410	6	37
β-strand	413	1	38
β-strand	417	1	38
β-strand	418-420	3	37
α-helix	421-422	2
β-strand	423	1	39
β-strand	428	1	39
α-helix	433	1
β-strand	434-438	5	37
β-strand	453-458	6	37
α-helix	460-472	13
β-strand	475-480	6	37
β-strand	489	1	40
β-strand	494	1	40
α-helix	497-502	6
β-strand	508-510	3	37
α-helix	519-521	3
β-strand	524-525	2	37
β-strand	531-536	6	41
β-strand	537-538	2	42
α-helix	556-566	11
α-helix	605-611	7
α-helix	632-653	22
α-helix	669-672	4
α-helix	680-681	2
β-strand	683-684	2	43
α-helix	690-695	6
α-helix	700-705	6
α-helix	714-723	10
β-strand	728-729	2	43
β-strand	730-732	3	41
α-helix	733-741	9
β-strand	749-750	2	42
β-strand	757-761	5	41
β-strand	765-766	2	37
α-helix	773-786	14
α-helix	788-793	6
α-helix	822-836	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	825	Rattus norvegicus	P35439 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	820	Rattus norvegicus	Q00960 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4PE5_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
DPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLQATSVTHKPNAIQMALSVCEDL
ISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVP
PYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTK
NVTALLMEARELEARVIILSASEDDAATVYRAAAMLDMTGSGYVWLVGEREISGNALRYA
PDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFK
RVLMSSKYADGVTGRVEFNEDGDRKFAQYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWP
GGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDT
SPGSPRHTVPQCCYGFCIDLLIKLARTMQFTYEVHLVADGKFGTQERVQNSNKKEWNGMM
GELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSCL
WLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSQSESTDALTLSSAMWFSWGVLLNSGIGEG
APRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYA
TVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQ
KCDLVTTGELFFRSGFGIGMRKDSPWKQQVSLSILKSHENGFMEDLDKTWVRYQECDSRS
NAPATLTCENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDANGAQ

Sequence of entity 2 (B, D), FASTA

>4PE5_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
RSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRIC
DLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQF
GPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLD
MSLDDGDCKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDT
DTVPSEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHE
KRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQM
KYYVWPRMTQDDHLSIVTLEEAPFVIVESVDPLSGTCMRNTVPCQKRIISENKTDEEPGY
IKKCCKGFCIDILKKISKSVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGS
LTINEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSACVWVMMFVMLLIVSAV
AVFVFEYFSPVGYNRSLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMV
SVWAFFAVIFLASYTANLAAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTE
RNIRNNYAEMHAYMGKFNQRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIG
SGKVFASTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQ
LDCDNMAGVFYMLGAAMALSLITFISEHLFYWQFRHSFMG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8
GLY	Glycine	C2 H5 N O2	2
W	Tungsten ion	W	84
GLU	Glutamic acid	C5 H9 N O4	2
QEL	4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol	C21 H27 N O2	2

Primary citation

Crystal structure of a heterotetrameric NMDA receptor ion channel. Karakas, E., Furukawa, H. Science (2014) 344:992-997. DOI 10.1126/science.1251915 · PubMed

Other PDB entries of the same protein (UniProt P35439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1PB7 1.35 Å, Crystal structure of the NR1 ligand binding core in complex with glycine at 1.35 Å…
1Y20 1.4 Å, Crystal structure of the NR1 ligand-binding core in complex with ACPC
1PB8 1.45 Å, Crystal structure of the NR1 ligand binding core in complex with D-serine at 1.45 Å…
1Y1Z 1.5 Å, Crystal structure of the NR1 ligand binding core in complex with ACBC
5U8C 1.6 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…
1PB9 1.6 Å, Crystal structure of the NR1 ligand binding core in complex with D-cycloserine at 1.60 Å…
6UZ6 1.66 Å, Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with…
5I57 1.7 Å, Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains
9NYZ 1.71 Å, Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with…
1Y1M 1.8 Å, Crystal structure of the NR1 ligand binding core in complex with cycloleucine
4NF8 1.86 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and…
6UZR 1.87 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…

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