4NF5: GluN1/GluN2A ligand-binding domain

Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and D-AP5. Determined by X-ray diffraction at 1.9 Å resolution. Released 12 Mar 2014.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 5,021
Mol. weight: 65.67 kDa
Ligands: GLY, 2JJ
Released: 12 Mar 2014

Explore 4NF5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NF5 contains 31 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: 16 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	18-21	4	1
α-helix	22-23	2
α-helix	27-30	4
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	136-137	2	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	180-187	8
α-helix	189-191	3
α-helix	192-198	7
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	253-254	2	1
α-helix	261-273	13
α-helix	276-280	5
α-helix	281-285	5

Chain B: 15 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	21-24	4	8
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
β-strand	116	1	11
α-helix	119-122	4
β-strand	126-127	2	8
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
β-strand	231-233	3	11
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

>4NF5_1 Glutamate receptor ionotropic, NMDA 1 (chains A)
GMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVP
QCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADM
IVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSS
VDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVT
TGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS

Sequence of entity 2 (B), FASTA

>4NF5_2 Glutamate receptor ionotropic, NMDA 2A (chains B)
SDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFC
IDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSE
VVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYP
YMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATT
GYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHN

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	1
2JJ	5-phosphono-D-norvaline	C5 H12 N O5 P	1

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

Primary citation

Structural Insights into Competitive Antagonism in NMDA Receptors. Jespersen, A., Tajima, N., Fernandez-Cuervo, G. et al. Neuron (2014) 81:366-378. DOI 10.1016/j.neuron.2013.11.033 · 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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