5VII: Glutamate receptor ionotropic, NMDA 1

Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-(3-fluoropropyl)phenyl-ACEPC. Determined by X-ray diffraction at 1.95 Å resolution. Released 26 Apr 2017.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 4,813
Mol. weight: 65.76 kDa
Ligands: 5DY, GLY
Released: 26 Apr 2017

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

Secondary structure: helices and β-sheets

5VII contains 36 α-helices and 42 β-strands across 2 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: 15 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	13	1	2
β-strand	17	1	2
β-strand	18-20	3	1
α-helix	21-23	3
β-strand	32	1	3
β-strand	38	1	3
β-strand	42-46	5	1
β-strand	59-64	6	1
α-helix	66-78	13
β-strand	82-86	5	1
β-strand	95-97	3	4
β-strand	104-106	3	4
α-helix	108-115	8
β-strand	120-121	2	1
β-strand	126	1	5
α-helix	129-132	4
β-strand	135-137	3	1
α-helix	138	1
α-helix	140	1
β-strand	142-151	10	5
α-helix	162-165	4
β-strand	168	1	6
β-strand	171	1	6
β-strand	173-174	2	5
β-strand	176	1	7
α-helix	180-186	7
α-helix	189-191	3
α-helix	192-199	8
β-strand	203	1	7
α-helix	206-214	9
β-strand	220-224	5	5
α-helix	225-234	10
β-strand	238-240	3	5
β-strand	246-250	5	5
β-strand	253-255	3	1
α-helix	261-273	13
α-helix	276-280	5
α-helix	281-285	5

Chain B: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	8
β-strand	16	1	9
β-strand	20	1	9
β-strand	21-23	3	8
α-helix	32-33	2
β-strand	37-44	8	8
β-strand	52-60	9	8
α-helix	62-70	9
α-helix	71-75	5
β-strand	77-82	6	8
β-strand	91-92	2	10
β-strand	95-96	2	10
α-helix	98-104	7
β-strand	110-111	2	8
α-helix	115	1
β-strand	116	1	11
α-helix	117	1
α-helix	119-124	6
β-strand	126-127	2	8
α-helix	128-130	3
β-strand	132-141	10	11
α-helix	152-155	4
α-helix	157-159	3
α-helix	163-164	2
β-strand	166-167	2	11
α-helix	173-181	9
α-helix	183-189	7
α-helix	190-192	3
α-helix	197-205	9
β-strand	211-215	5	11
α-helix	216-224	9
α-helix	227-229	3
β-strand	231-233	3	11
α-helix	234-235	2
α-helix	236-238	3
β-strand	240-245	6	11
β-strand	248-249	2	8
α-helix	256-268	13
α-helix	271-279	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A	protein	292	Rattus norvegicus	P35439 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2A	B	protein	283	Rattus norvegicus	Q00959 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5VII_1 Glutamate receptor ionotropic, NMDA 1 (chains A)
GMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVP
QCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADM
IVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSS
VDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVT
TGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS

Sequence of entity 2 (B), FASTA

>5VII_2 Glutamate receptor ionotropic, NMDA 2A (chains B)
SDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFC
IDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSE
VVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYP
YMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATT
GYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHN

Ligands and cofactors

ID	Name	Formula	Copies
5DY	5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl)phenyl]-1H-pyrazole-3-carb…	C16 H18 F N3 O4	1
GLY	Glycine	C2 H5 N O2	1

Water and common crystallization additives (TRS, PEG) are not listed.

Primary citation

Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits. Lind, G.E., Mou, T.C., Tamborini, L. et al. Proc Natl Acad Sci U S A (2017) 114:E6942-E6951. DOI 10.1073/pnas.1707752114 · 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…

Browse structure collections

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