1PBQ: NR1 ligand binding core

Crystal structure of the NR1 ligand binding core in complex with 5,7-dichlorokynurenic acid (DCKA) at 1.90 Å resolution. Determined by X-ray diffraction at 1.9 Å resolution. Released 29 Jul 2003.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 4,613
Mol. weight: 67.2 kDa
Ligands: DK1
Released: 29 Jul 2003

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

Secondary structure: helices and β-sheets

1PBQ contains 27 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: 13 helices, 19 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	42-45	4	1
β-strand	60-64	5	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	120-126	7	1
α-helix	129-132	4
β-strand	136-137	2	1
β-strand	142-151	10	1
α-helix	162-165	4
β-strand	173-174	2	1
β-strand	176	1	5
α-helix	180-187	8
α-helix	189-191	3
α-helix	192-198	7
β-strand	203	1	5
α-helix	206-214	9
β-strand	220-224	5	1
α-helix	225-234	10
β-strand	238-254	17	1
α-helix	261-273	13
α-helix	276-284	9

Chain B: 14 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	6
β-strand	13	1	7
β-strand	17	1	7
β-strand	18-21	4	6
α-helix	27-30	4
β-strand	32	1	8
β-strand	38	1	8
β-strand	42-44	3	6
β-strand	61-64	4	6
α-helix	66-77	12
β-strand	82-86	5	6
β-strand	95	1	9
β-strand	106	1	9
α-helix	108-115	8
β-strand	120-121	2	6
α-helix	125	1
β-strand	126	1	10
α-helix	127	1
α-helix	129-132	4
β-strand	136-137	2	6
β-strand	142-151	10	10
α-helix	162-165	4
β-strand	168	1	11
β-strand	171	1	11
β-strand	173-174	2	10
β-strand	176	1	12
α-helix	180-187	8
α-helix	189-191	3
α-helix	192-198	7
β-strand	203	1	12
α-helix	206-214	9
β-strand	220-224	5	10
α-helix	225-234	10
β-strand	238-250	13	10
β-strand	253-254	2	6
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, B	protein	292	Rattus norvegicus	P35439 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1PBQ_1 N-methyl-D-aspartate Receptor Subunit 1 (chains A, B)
GMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVP
QCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADM
IVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSS
VDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVT
TGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDS

Ligands and cofactors

ID	Name	Formula	Copies
DK1	5,7-dichloro-4-hydroxyquinoline-2-carboxylic acid	C10 H5 Cl2 N O3	2

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…
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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