1PB9: NR1 ligand binding core

Crystal structure of the NR1 ligand binding core in complex with D-cycloserine at 1.60 Å resolution. Determined by X-ray diffraction at 1.6 Å resolution. Released 24 Jun 2003.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 2,436
Mol. weight: 33.43 kDa
Ligands: 4AX
Released: 24 Jun 2003

Explore 1PB9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1PB9 contains 15 α-helices and 24 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: 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	18-21	4	1
α-helix	22-23	2
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	180-186	7
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	253-255	3	1
α-helix	261-273	13
α-helix	276-284	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-methyl-D-aspartate Receptor Subunit 1	A	protein	292	Rattus norvegicus	P35439 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1PB9_1 N-methyl-D-aspartate Receptor Subunit 1 (chains A)
GMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVP
QCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADM
IVAPLTINTERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSS
VDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVT
TGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS

Ligands and cofactors

ID	Name	Formula	Copies
4AX	(r)-4-amino-isoxazolidin-3-one	C3 H6 N2 O2	1

Primary citation

Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core. Furukawa, H., Gouaux, E. EMBO J (2003) 22:2873-2885. DOI 10.1093/emboj/cdg303 · 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…
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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