5EWM: NMDA glutamate receptor subunit

Crystal structure of amino terminal domains of the nmda receptor subunit GLUN1 and GLUN2B in complex with evt-101. Determined by X-ray diffraction at 2.76 Å resolution. Released 2 Mar 2016.

Method: X-ray diffraction
Resolution: 2.76 Å
Organisms: Xenopus laevis, Homo sapiens
Chains: 4
Atoms: 11,534
Mol. weight: 173.21 kDa
Ligands: 5SM, NAG
Released: 2 Mar 2016

Explore 5EWM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EWM contains 70 α-helices and 71 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: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	24	1
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	93-95	3
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	148-158	11
β-strand	162-168	7	2
α-helix	171-184	14
β-strand	211-218	8	2
α-helix	226-234	9
β-strand	239-243	5	2
α-helix	246-258	13
β-strand	267-269	3	2
α-helix	273-275	3
α-helix	277-282	6
α-helix	283-284	2
β-strand	288-292	5	2
α-helix	298-316	19
α-helix	323-326	4
α-helix	339-347	9
β-strand	351-354	4	3
β-strand	357-359	3	3
β-strand	360-361	2	4
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	47-50	4
β-strand	65-73	9	5
α-helix	78-91	14
β-strand	94-100	7	5
α-helix	107-119	13
β-strand	123-127	5	5
α-helix	128-131	4
β-strand	143-145	3	5
α-helix	150-164	15
β-strand	168-173	6	6
α-helix	179-191	13
β-strand	198-204	7	6
α-helix	215-221	7
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	278-282	5	6
α-helix	289-311	23
α-helix	315-318	4
α-helix	324-327	4
α-helix	328-330	3
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	373-379	7	6
β-strand	384-386	3	6

Chain C: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	24	1
β-strand	25-33	9	9
α-helix	36-53	18
β-strand	58-66	9	9
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	9
α-helix	105-113	9
β-strand	118-120	3	9
α-helix	126-129	4
β-strand	137-139	3	9
α-helix	144-147	4
α-helix	148-158	11
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	277-282	6
α-helix	283-284	2
β-strand	288-292	5	10
α-helix	298-316	19
α-helix	323-326	4
α-helix	339-347	9
β-strand	351-354	4	11
β-strand	357-359	3	11
β-strand	360-361	2	12
β-strand	366	1	9
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
β-strand	402	1	13
β-strand	406	1	13

Chain D: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	14
α-helix	47-51	5
β-strand	65-73	9	14
α-helix	78-91	14
β-strand	94-100	7	14
α-helix	107-119	13
β-strand	123-127	5	14
α-helix	128-130	3
β-strand	143-145	3	14
α-helix	150-164	15
β-strand	168-174	7	15
α-helix	179-191	13
β-strand	198-205	8	15
α-helix	215-220	6
β-strand	227-231	5	15
α-helix	234-246	13
β-strand	255-258	4	15
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	15
α-helix	289-311	23
α-helix	315-318	4
α-helix	325-330	6
α-helix	336-339	4
β-strand	351	1	16
β-strand	356	1	14
β-strand	357	1	16
β-strand	362-367	6	15
β-strand	373-379	7	15
β-strand	384-386	3	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NMDA glutamate receptor subunit	A, C	protein	390	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	364	Homo sapiens	Q13224 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5EWM_1 NMDA glutamate receptor subunit (chains A, C)
DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDL
ISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVP
PYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQL
SYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMT
GAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENI
TDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKL
VQVGIFNGSYIIQNDRKIIWPGGETELVPR

Sequence of entity 2 (B, D), FASTA

>5EWM_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
SPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMS
DRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSI
EQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLD
DGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVP
AEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIY
QSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYV
WPRM

Ligands and cofactors

ID	Name	Formula	Copies
5SM	5-[3-[bis(fluoranyl)methyl]-4-fluoranyl-phenyl]-3-[(2-methylimidazol-1-yl)methy…	C16 H13 F3 N4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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

Primary citation

A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists. Stroebel, D., Buhl, D.L., Knafels, J.D. et al. Mol Pharmacol (2016) 89:541-551. DOI 10.1124/mol.115.103036 · PubMed

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…
6E7W 2.67 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
5EWJ 2.77 Å, Crystal structure of amino terminal domains of the nmda receptor subunit GLUN1 and…

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