1Y20: NR1 ligand-binding core

Crystal structure of the NR1 ligand-binding core in complex with ACPC. Determined by X-ray diffraction at 1.4 Å resolution. Released 12 Jul 2005.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 2,681
Mol. weight: 33.44 kDa
Ligands: 1AC
Released: 12 Jul 2005

Explore 1Y20 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Y20 contains 14 α-helices and 23 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: 14 helices, 23 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
β-strand	32	1	3
α-helix	37	1
β-strand	38	1	3
α-helix	39-40	2
β-strand	42-47	6	1
β-strand	58-64	7	1
α-helix	66-77	12
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
α-helix	125	1
β-strand	126	1	5
α-helix	127	1
α-helix	129-132	4
β-strand	135-137	3	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	180-185	6
α-helix	189-199	11
β-strand	203	1	7
α-helix	206-214	9
β-strand	220-224	5	5
α-helix	225-234	10
β-strand	238-250	13	5
β-strand	253-255	3	1
α-helix	261-273	13
α-helix	276-284	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate [NMDA] receptor subunit zeta 1	A	protein	292	Rattus norvegicus	P35439 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1Y20_1 Glutamate [NMDA] receptor subunit zeta 1 (chains A)
GMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVP
QCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADM
IVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSS
VDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVT
TGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS

Ligands and cofactors

ID	Name	Formula	Copies
1AC	1-aminocyclopropanecarboxylic acid	C4 H7 N O2	1

Primary citation

Mechanism of Partial Agonist Action at the NR1 Subunit of NMDA Receptors. Inanobe, A., Furukawa, H., Gouaux, E. Neuron (2005) 47:71-84. DOI 10.1016/j.neuron.2005.05.022 · 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…
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…
4KCC 1.89 Å, Crystal Structure of the NMDA Receptor GluN1 Ligand Binding Domain Apo State

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