6E7W: Glutamate receptor ionotropic, NMDA 1

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-115. Determined by X-ray diffraction at 2.67 Å resolution. Released 30 Jan 2019.

Method: X-ray diffraction
Resolution: 2.67 Å
Organisms: Xenopus laevis, Rattus norvegicus
Chains: 4
Atoms: 11,315
Mol. weight: 172.95 kDa
Ligands: HXM, NAG
Released: 30 Jan 2019

Explore 6E7W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E7W contains 68 α-helices and 70 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: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	25-33	9	1
α-helix	36-52	17
β-strand	58-66	9	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	144-147	4
α-helix	148-157	10
β-strand	162-168	7	2
α-helix	171-184	14
β-strand	211-218	8	2
α-helix	226-233	8
β-strand	239-243	5	2
α-helix	246-258	13
β-strand	267-269	3	2
α-helix	273-275	3
α-helix	277-280	4
α-helix	283-284	2
β-strand	288-292	5	2
α-helix	298-316	19
α-helix	322-326	5
α-helix	339-347	9
β-strand	351-354	4	3
β-strand	357-359	3	3
β-strand	360-361	2	4
α-helix	366	1
β-strand	367-368	2	4
β-strand	372-378	7	2
β-strand	381-388	8	2
β-strand	393-395	3	2
α-helix	399-400	2

Chain B: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	5
α-helix	47-52	6
β-strand	65-73	9	5
α-helix	78-90	13
β-strand	94-100	7	5
α-helix	107-118	12
β-strand	123-127	5	5
α-helix	128-131	4
α-helix	133-134	2
β-strand	143-145	3	5
α-helix	150-163	14
β-strand	168-173	6	6
α-helix	179-191	13
β-strand	198-204	7	6
α-helix	215-220	6
β-strand	227-231	5	6
α-helix	234-246	13
β-strand	255-258	4	6
α-helix	260-263	4
α-helix	274	1
β-strand	278-281	4	6
α-helix	289-311	23
α-helix	315-318	4
α-helix	327-330	4
α-helix	336-339	4
β-strand	343-344	2	7
β-strand	347-348	2	7
β-strand	351	1	8
β-strand	356	1	5
β-strand	357	1	8
β-strand	362-367	6	6
β-strand	373-380	8	6
β-strand	383-386	4	6

Chain C: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	25-33	9	9
α-helix	36-52	17
β-strand	58-66	9	9
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	9
α-helix	93-96	4
α-helix	105-114	10
β-strand	118-120	3	9
α-helix	126-129	4
β-strand	137-139	3	9
α-helix	144-147	4
α-helix	148-157	10
β-strand	162-168	7	10
α-helix	171-184	14
β-strand	211-218	8	10
α-helix	226-234	9
β-strand	239-243	5	10
α-helix	246-258	13
β-strand	267-269	3	10
α-helix	273-275	3
α-helix	278-282	5
α-helix	284	1
β-strand	288-292	5	10
α-helix	298-317	20
α-helix	322-326	5
α-helix	339-347	9
β-strand	351-354	4	11
β-strand	357-359	3	11
β-strand	360-361	2	12
α-helix	366	1
β-strand	367-368	2	12
β-strand	372-378	7	10
β-strand	381-388	8	10
β-strand	393-395	3	10
α-helix	399-400	2

Chain D: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	13
α-helix	47-51	5
α-helix	56-59	4
β-strand	65-73	9	13
α-helix	78-90	13
β-strand	94-100	7	13
α-helix	107-119	13
β-strand	123-127	5	13
α-helix	128-131	4
β-strand	143-145	3	13
α-helix	150-163	14
β-strand	168-173	6	14
α-helix	179-191	13
β-strand	198-204	7	14
α-helix	215-220	6
β-strand	227-231	5	14
α-helix	234-246	13
β-strand	255-258	4	14
α-helix	260-263	4
α-helix	274	1
β-strand	278-281	4	14
α-helix	289-311	23
α-helix	336-339	4
β-strand	343	1	15
β-strand	348	1	15
β-strand	351	1	16
β-strand	356	1	13
β-strand	357	1	16
β-strand	362-367	6	14
β-strand	373-380	8	14
β-strand	383-386	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	385	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	363	Rattus norvegicus	Q00960 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6E7W_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDL
ISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVP
PYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQL
SYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMT
GAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENI
TDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKL
VQVGIFNGSYIIQNDRKIIWPGGET

Sequence of entity 2 (B, D), FASTA

>6E7W_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
PPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSD
RKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIE
QQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDD
GDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPS
EFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQ
SNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVW
PRM

Ligands and cofactors

ID	Name	Formula	Copies
HXM	N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propan-2-yl)amino}-2-hydroxypropoxy…	C21 H28 Cl2 N2 O4 S	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Water and common crystallization additives (CL, NA) are not listed.

Primary citation

Structural elements of a pH-sensitive inhibitor binding site in NMDA receptors. Regan, M.C., Furukawa, H. Nat Commun (2019) 10:321.

Other PDB entries of the same protein (UniProt A0A1L8F5J9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3QEK 2.0 Å, Crystal structure of amino terminal domain of the NMDA receptor subunit GluN1
6E7R 2.1 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7U 2.27 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7T 2.31 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7X 2.58 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
3QEL 2.6 Å, Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and…
6E7V 2.6 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
5TQ0 2.7 Å, Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and…
6E7S 2.72 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
9Q3Y 2.74 Å, GluN1b-GluN2B ATD in complex with radiprodil
5EWM 2.76 Å, Crystal structure of amino terminal domains of the nmda receptor subunit GLUN1 and…
5EWJ 2.77 Å, Crystal structure of amino terminal domains of the nmda receptor subunit GLUN1 and…

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