3JPW: Glutamate [NMDA] receptor subunit epsilon-2

Crystal structure of amino terminal domain of the NMDA receptor subunit NR2B. Determined by X-ray diffraction at 2.8 Å resolution. Released 8 Dec 2009.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 2,843
Mol. weight: 42.35 kDa
Ligands: NAG
Released: 8 Dec 2009

Explore 3JPW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JPW contains 13 α-helices and 18 β-strands across 1 chain. 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: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	1
α-helix	53-55	3
β-strand	67-73	7	1
α-helix	78-91	14
β-strand	97-101	5	1
α-helix	107-119	13
β-strand	122-127	6	1
α-helix	128-131	4
β-strand	142-145	4	1
α-helix	150-162	13
β-strand	168-173	6	2
α-helix	179-191	13
β-strand	198-204	7	2
α-helix	217-220	4
β-strand	227-231	5	2
α-helix	234-245	12
β-strand	255-258	4	2
α-helix	260-263	4
α-helix	274	1
β-strand	277-281	5	2
α-helix	289-311	23
α-helix	315-318	4
α-helix	329-339	11
β-strand	343-344	2	3
β-strand	347-348	2	3
β-strand	351	1	4
β-strand	356	1	1
β-strand	357	1	4
β-strand	362-367	6	2
β-strand	373-379	7	2
β-strand	384-386	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate [NMDA] receptor subunit epsilon-2	A	protein	363	Rattus norvegicus	Q00960 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3JPW_1 Glutamate [NMDA] receptor subunit epsilon-2 (chains A)
PPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSD
RKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIE
QQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDD
GDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPS
EFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQ
SNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVW
PRM

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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

Primary citation

Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit. Karakas, E., Simorowski, N., Furukawa, H. EMBO J (2009) 28:3910-3920. DOI 10.1038/emboj.2009.338 · PubMed

Other PDB entries of the same protein (UniProt Q00960 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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…
9OBX 2.59 Å, glutamate/glycine and Ca2+-bound GluN1a/2B NMDAR
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…
9OC2 2.69 Å, Ca2+-bound GluN1a/2B NMDAR (S5)
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
9OC1 2.76 Å, Ca2+-bound GluN1a/2B NMDAR (S4)

Browse structure collections

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