1Y1M: NR1 ligand binding core

Crystal structure of the NR1 ligand binding core in complex with cycloleucine. Determined by X-ray diffraction at 1.8 Å resolution. Released 12 Jul 2005.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 4,900
Mol. weight: 66.94 kDa
Ligands: AC5
Released: 12 Jul 2005

Explore 1Y1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Y1M contains 29 α-helices and 46 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: 13 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	42-46	5	1
β-strand	59-64	6	1
α-helix	66-77	12
β-strand	82-86	5	1
β-strand	95-96	2	4
β-strand	105-106	2	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
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	238-250	13	5
β-strand	253-254	2	1
α-helix	261-273	13
α-helix	276-284	9

Chain B: 16 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	8
β-strand	13	1	9
β-strand	17	1	9
β-strand	18-21	4	8
α-helix	28-30	3
β-strand	32	1	10
α-helix	37	1
β-strand	38	1	10
α-helix	39-40	2
β-strand	42-46	5	8
β-strand	59-64	6	8
α-helix	66-77	12
β-strand	82-86	5	8
β-strand	95	1	11
β-strand	106	1	11
α-helix	108-115	8
β-strand	120-121	2	8
β-strand	126	1	12
α-helix	129-132	4
β-strand	136-137	2	8
α-helix	138	1
α-helix	140	1
β-strand	142-151	10	12
α-helix	162-165	4
β-strand	168	1	13
β-strand	171	1	13
β-strand	173-174	2	12
β-strand	176	1	14
α-helix	180-187	8
α-helix	189-191	3
α-helix	192-198	7
β-strand	203	1	14
α-helix	206-214	9
β-strand	220-224	5	12
α-helix	225-234	10
β-strand	238-250	13	12
β-strand	253-254	2	8
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, B	protein	292	Rattus norvegicus	P35439 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1Y1M_1 Glutamate [NMDA] receptor subunit zeta 1 (chains A, B)
GMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVP
QCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADM
IVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSS
VDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVT
TGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS

Ligands and cofactors

ID	Name	Formula	Copies
AC5	1-aminocyclopentanecarboxylic acid	C6 H11 N O2	2

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…
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…
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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