8y1v

Structure of GluN1b-GluN2D NMDA receptor in complex with competitive antagonist R-CPP and allosteric inhibitor YY-23

Method: ELECTRON MICROSCOPY D_max: 179.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 6 of Glutamate receptor ionotropic, NMDA 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–868 Chain C； UniProt 1–868	Not recorded	Glutamate receptor ionotropic, NMDA 2D × 2 （O15399） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 A1LW8 (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-methyl-4-[(1~{R},2~{R},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{R})-7,9,13,18-tetramethyl-16-oxidanyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-yl]butoxy]oxane-3,4,5-triol × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.20 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8Y1V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10EY SK5B-Matured in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–838（838 aa） Chain C 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
10EZ SK3D-Germline in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–841（841 aa） Chain C 1–841（841 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.76 Å
10FD SK5G-Matured in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–841（841 aa） Chain C 1–841（841 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
10FE OX1-Germline in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–841（841 aa） Chain C 1–841（841 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.55 Å
10FF SK5A-Matured glycine/glutamate in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–841（841 aa） Chain C 1–841（841 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.06 Å
10FL SK5G-Germline Deposited 2026-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–841（841 aa） Chain C 1–841（841 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.81 Å
10FN SK5A-Germline in complex with GluN1-GluN2B, full refinement Deposited 2026-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–841（841 aa） Chain C 1–841（841 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.52 Å
10FO SK5B-Germline in complex with GluN1-GluN2B, full refinement Deposited 2026-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–841（841 aa） Chain C 1–841（841 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.46 Å
2HQW Crystal Structure of Ca2+/Calmodulin bound to NMDA Receptor NR1C1 peptide Deposited 2006-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 875–898（24 aa） Fragment：C-TERMINAL TAIL, C1 REGION	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277.15 K；7% PEG 6000, 5mM CaCl2, 100 mM sodium acetate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.90 Å R-free 0.248
2NR1 TRANSMEMBRANE SEGMENT 2 OF NMDA RECEPTOR NR1, NMR, 10 STRUCTURES Deposited 1997-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 599–621（23 aa） Fragment：TRANSMEMBRANE SEGMENT 2	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；303 K	Resolution not provided
3BYA Structure of a Calmodulin Complex Deposited 2008-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 875–898（24 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；17-19% PEG 3350, 0.120mM Ammonium Phosphate, 15% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.85 Å R-free 0.232
5H8F Structure of the apo human GluN1/GluN2A LBD Deposited 2015-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 394–544（151 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800 Chain B 663–800（138 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800	Not recorded	GOL GLYCEROL × 6 GLU GLUTAMIC ACID × 1 GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)	Resolution 1.81 Å R-free 0.207
5H8H Structure of the human GluN1/GluN2A LBD in complex with GNE3419 Deposited 2015-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 415–565（151 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800 Chain B 684–821（138 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800	Not recorded	ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 CA CALCIUM ION × 1 GLY GLYCINE × 1 5YC 7-[[ethyl(phenyl)amino]methyl]-2-methyl-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)	Resolution 2.23 Å R-free 0.227
5H8N Structure of the human GluN1/GluN2A LBD in complex with NAM Deposited 2015-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 394–544（151 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800 Chain B 663–800（138 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800	Not recorded	GLU GLUTAMIC ACID × 1 5YD 4-[[(4-fluorophenyl)sulfonylamino]methyl]-~{N}-(pyridin-3-ylmethyl)benzamide × 1 CA CALCIUM ION × 1 GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)	Resolution 2.50 Å R-free 0.236
5H8Q Structure of the human GluN1/GluN2A LBD in complex with GNE8324 Deposited 2015-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 394–544（151 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800 Chain B 663–800（138 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800	Not recorded	ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 GLY GLYCINE × 1 5YE 6-[[ethyl-(4-fluorophenyl)amino]methyl]-2,3-dihydro-1~{H}-cyclopenta[3,4][1,3]thiazolo[1,4-~{a}]pyrimidin-8-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)	Resolution 1.90 Å R-free 0.209
5I2K Structure of the human GluN1/GluN2A LBD in complex with 7-{[ethyl(4-fluorophenyl)amino]methyl}-N,2-dimethyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide (compound 19) Deposited 2016-02-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 415–565（151 aa） Fragment：UNP residues 415-565, GT linker, UNP residues 684-821 Chain B 684–821（138 aa） Fragment：UNP residues 415-565, GT linker, UNP residues 684-821	Not recorded	GLU GLUTAMIC ACID × 1 GLY GLYCINE × 1 67H 7-{[ethyl(4-fluorophenyl)amino]methyl}-N,2-dimethyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)	Resolution 2.86 Å R-free 0.256
5I2N Structure of the human GluN1/GluN2A LBD in complex with N-ethyl-7-{[2-fluoro-3-(trifluoromethyl)phenyl]methyl}-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide (compound 29) Deposited 2016-02-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 415–565（151 aa） Fragment：UNP residues 415-565, GT linker, UNP residues 684-821 Chain B 684–821（138 aa） Fragment：UNP residues 415-565, GT linker, UNP residues 684-821	Not recorded	CA CALCIUM ION × 1 GLU GLUTAMIC ACID × 1 67J N-ethyl-7-{[2-fluoro-3-(trifluoromethyl)phenyl]methyl}-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)	Resolution 2.12 Å R-free 0.223
5KCJ Structure of the human GluN1/GluN2A LBD in complex with GNE6901 Deposited 2016-06-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 415–565（151 aa） Fragment：Ligand binding domain (UNP residues 415-565, GT linker, UNP residues 684-821) Chain B 684–821（138 aa） Fragment：Ligand binding domain (UNP residues 415-565, GT linker, UNP residues 684-821)	Not recorded	ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 GLY GLYCINE × 1 6RM 7-[(4-fluoranylphenoxy)methyl]-3-[(1~{R},2~{R})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate	Resolution 2.09 Å R-free 0.225
5KDT Structure of the human GluN1/GluN2A LBD in complex with GNE0723 Deposited 2016-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 415–565（151 aa） Fragment：Ligand binding domain (UNP residues 415-565, GT linker, UNP residues 684-821) Chain B 684–821（138 aa） Fragment：Ligand binding domain (UNP residues 415-565, GT linker, UNP residues 684-821)	Not recorded	ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 6RV (1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl)pyrazol-1-yl]methyl]-5-oxidanylidene-2-(trifluoromethyl)-[1,3]thiazolo[3,2-a]pyrimidin-3-yl]cyclopropane-1-carbonitrile × 1 GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate	Resolution 2.44 Å R-free 0.240
5TP9 Structure of the human GluN1/GluN2A LBD in complex with compound 2 (GNE9178) Deposited 2016-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 415–565（151 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800 Chain B 684–821（138 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800	Not recorded	ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 7H0 7-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-N-ethyl-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide × 1 CA CALCIUM ION × 1 GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate	Resolution 2.40 Å R-free 0.237
5TPA Structure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500) Deposited 2016-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 415–565（151 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800 Chain B 684–821（138 aa） Fragment：UNP residues 394-544, GT linker, UNP residues 663-800	Not recorded	GLU GLUTAMIC ACID × 1 7H2 (1R,2R)-2-(2-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-6-yl)cyclopropane-1-carbonitrile × 1 GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate	Resolution 2.48 Å R-free 0.241
6IRA Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 7.8 Deposited 2018-11-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Mutation：G612R Mutation：G612R	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；Solutions were made fresh. cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging in liquid ethane.	Resolution 4.50 Å
6IRF Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 6.3, Class I Deposited 2018-11-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Mutation：G612R Mutation：G612R	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.3；Solutions were made fresh. cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging in liquid ethane	Resolution 5.10 Å
6IRG Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 6.3, Class II Deposited 2018-11-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Mutation：G612R Mutation：G612R	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.3；Solutions were made fresh. cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging in liquid ethane	Resolution 5.50 Å
6IRH Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 6.3, Class III Deposited 2018-11-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Mutation：G612R Mutation：G612R	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.3；Solutions were made fresh. cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging in liquid ethane	Resolution 7.80 Å
7EOQ Structure of the human GluN1/GluN2A NMDA receptor in the glycine/CPP bound state Deposited 2021-04-22	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–847（847 aa） Chain D 1–847（847 aa）	Mutation：E698C Mutation：E698C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
7EOR Structure of the human GluN1/GluN2A NMDA receptor in the glycine/glutamate/GNE-6901 bound state Deposited 2021-04-22	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–847（847 aa） Chain D 1–847（847 aa）	Mutation：E698C Mutation：E698C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 6RM 7-[(4-fluoranylphenoxy)methyl]-3-[(1~{R},2~{R})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7EOS Structure of the human GluN1/GluN2A NMDA receptor in the glycine/glutamate bound state Deposited 2021-04-22	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–847（847 aa） Chain D 1–847（847 aa）	Mutation：E698C Mutation：E698C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7EOT Structure of the human GluN1/GluN2A NMDA receptor in the CGP-78608/glutamate bound state Deposited 2021-04-22	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–847（847 aa） Chain D 1–847（847 aa）	Mutation：E698C Mutation：E698C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 J86 [(1S)-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylamino]ethyl]phosphonic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7EOU Structure of the human GluN1/GluN2A NMDA receptor in the glycine/glutamate/GNE-6901/9-AA bound state Deposited 2021-04-22	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–847（847 aa） Chain D 1–847（847 aa）	Mutation：E698C Mutation：E698C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 AA 9-AMINOACRIDINE × 1 6RM 7-[(4-fluoranylphenoxy)methyl]-3-[(1~{R},2~{R})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7EU7 Structure of the human GluN1-GluN2A NMDA receptor in complex with S-ketamine, glycine and glutamate Deposited 2021-05-16	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 JC9 (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7EU8 Structure of the human GluN1-GluN2B NMDA receptor in complex with S-ketamine,glycine and glutamate Deposited 2021-05-16	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 JC9 (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.07 Å
7YFF Structure of GluN1a-GluN2D NMDA receptor in complex with agonist glycine and competitive antagonist CPP. Deposited 2022-07-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–840（840 aa） Chain C 1–840（840 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 GLY GLYCINE × 2 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 3.60 Å
7YFL Structure of GluN1a-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Deposited 2022-07-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 3.90 Å
7YFM Structure of GluN1b-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Deposited 2022-07-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–868（868 aa） Chain C 1–868（868 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 5.10 Å
7YFO Structure of GluN1a E698C-GluN2D NMDA receptor in cystines crosslinked state. Deposited 2022-07-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Mutation：E698C Mutation：E698C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 6.40 Å
7YFR Structure of GluN1a E698C-GluN2D NMDA receptor in cystines non-crosslinked state. Deposited 2022-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Mutation：E698C Mutation：E698C	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 5.10 Å
8E92 D-cycloserine and glutamate bound Human GluN1a-GluN2C NMDA receptor in intact conformation Deposited 2022-08-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
8E93 D-cycloserine and glutamate bound Human GluN1a-GluN2C NMDA receptor in splayed conformation Deposited 2022-08-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.71 Å
8E94 PYD-106-bound Human GluN1a-GluN2C NMDA receptor in intact conformation Deposited 2022-08-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 IWB methyl 4-[(2~{R})-3-ethanoyl-1-[2-(2-methyl-1~{H}-indol-3-yl)ethyl]-4-oxidanyl-5-oxidanylidene-2~{H}-pyrrol-2-yl]benzoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
8E96 Glycine and glutamate bound Human GluN1a-GluN2D NMDA receptor Deposited 2022-08-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 19–847（829 aa） Chain C 19–847（829 aa）	Mutation：C22S, R844N, R845G, K846A Mutation：C22S, R844N, R845G, K846A	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
8E97 PYD-106-bound Human GluN1a-GluN2C NMDA receptor in splayed conformation Deposited 2022-08-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.19 Å
8E98 D-cycloserine and glutamate bound Human GluN1a-GluN2C NMDA receptor in nanodisc - intact conformation Deposited 2022-08-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.75 Å
8E99 Human GluN1a-GluN2A-GluN2C triheteromeric NMDA receptor in complex with Nb-4 Deposited 2022-08-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–843（843 aa） Chain C 1–843（843 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.24 Å
8JIZ Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab5F6 in two fab bind conformation Deposited 2023-05-29	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–847（847 aa） Chain D 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8JJ0 Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab5F6 in one fab bind conformation Deposited 2023-05-29	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–847（847 aa） Chain D 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
8JJ1 Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 in two fab conformation Deposited 2023-05-29	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–847（847 aa） Chain D 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.77 Å
8JJ2 Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 in one fab conformation Deposited 2023-05-29	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–847（847 aa） Chain D 1–847（847 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
8USX Glycine-bound GluN1a-3A NMDA receptor Deposited 2023-10-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–843（821 aa） Chain C 23–843（821 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8UUE Glycine-bound GluN1a-3A LBD heterotetramer (local refinement) Deposited 2023-11-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 395–798（404 aa） Chain C 395–798（404 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
8VUH Human GluN1-2A IgG 003-102 splayed conformation Deposited 2024-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 27–841（815 aa） Chain C 26–841（816 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.42 Å
8VUJ Human GluN1-2A with Fab 003-102 Deposited 2024-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 27–841（815 aa） Chain C 26–841（816 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.92 Å
8VUL Human GluN1-2A with Fab 003-102 Local refinement of ATD Deposited 2024-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–393（369 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.83 Å
8VUN Human GluN1-2A With Fab 008-218 Deposited 2024-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 25–841（817 aa） Chain C 25–841（817 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.01 Å
8VUQ Human GluN1-2A with Fab 008-218 Local refinement of ATD Deposited 2024-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–393（369 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.85 Å
8VUR Human GluN1-2A with IgG 003-102 WT conformation Deposited 2024-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 27–841（815 aa） Chain C 27–841（815 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
8VUS Human GluN1-2A with IgG 007-168 Deposited 2024-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 23–798（776 aa） Chain C 23–798（776 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.99 Å
8VUT Human GluN1-2A with IgG 008-218 Deposited 2024-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 25–841（817 aa） Chain C 25–841（817 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8VUU Human GluN1-2B with Fab 007-168 Deposited 2024-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 23–838（816 aa） Chain C 23–838（816 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.05 Å
8VUV Human GluN1-2B with Fab 007-168 Local refinement of ATD Deposited 2024-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–393（371 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å
8ZH7 Crystal structure of N-terminal domain of N-methyl-D-aspartate receptor subunit NR1 in complex with patient-derived antibody Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 21–393（373 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES or HEPES, pH6.5-7.5, and 6-8 %w/v PEG20000	Resolution 3.50 Å R-free 0.227
8ZH7 Crystal structure of N-terminal domain of N-methyl-D-aspartate receptor subunit NR1 in complex with patient-derived antibody Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 21–393（373 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES or HEPES, pH6.5-7.5, and 6-8 %w/v PEG20000	Resolution 3.50 Å R-free 0.227
8ZH7 Crystal structure of N-terminal domain of N-methyl-D-aspartate receptor subunit NR1 in complex with patient-derived antibody Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 21–393（373 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES or HEPES, pH6.5-7.5, and 6-8 %w/v PEG20000	Resolution 3.50 Å R-free 0.227
8ZH7 Crystal structure of N-terminal domain of N-methyl-D-aspartate receptor subunit NR1 in complex with patient-derived antibody Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 21–393（373 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES or HEPES, pH6.5-7.5, and 6-8 %w/v PEG20000	Resolution 3.50 Å R-free 0.227
9D37 Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–847（825 aa） Chain C 23–847（825 aa）	Mutation：R844N, R845G, K846A Mutation：R844N, R845G, K846A	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
9D38 Open state of Gly-,Glu-,EU1622-240 bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–847（825 aa） Chain C 23–847（825 aa）	Mutation：R844N, R845G, K846A Mutation：R844N, R845G, K846A	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.95 Å
9D39 Gly-,PPDA- bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–847（825 aa） Chain C 23–847（825 aa）	Mutation：R844N, R845G, K846A Mutation：R844N, R845G, K846A	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2JL (2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9D3A Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR (Low-res) Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–847（825 aa） Chain C 23–847（825 aa）	Mutation：R844N, R845G, K846A Mutation：R844N, R845G, K846A	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.78 Å
9D3B Gly-,Glu-,(S)-DQP-997-74 bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–847（825 aa） Chain C 23–847（825 aa）	Mutation：R844N, R845G, K846A Mutation：R844N, R845G, K846A	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLU GLUTAMIC ACID × 2 A1A15 4-{(3R,5S)-5-(4-chlorophenyl)-3-[4-(4-chlorophenyl)-2-oxo-1,2-dihydroquinolin-3-yl]pyrazolidin-1-yl}-3,3-difluoro-4-oxobutanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.71 Å
9D3C Gly-,Glu-,(S)-(+)-ketamine bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–847（825 aa） Chain C 23–847（825 aa）	Mutation：R844N, R845G, K846A Mutation：R844N, R845G, K846A	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 GLU GLUTAMIC ACID × 2 JC9 (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
9GIB NMDA bound to compound 380 Deposited 2024-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 394–544（151 aa） Chain B 663–800（138 aa）	Not recorded	GOL GLYCEROL × 1 GLU GLUTAMIC ACID × 1 A1ILP (2~{R})-2-azanyl-3-[[3-(5-ethyl-1,2-oxazol-4-yl)-5-fluoranyl-phenyl]carbonylamino]propanoic acid × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；282.15 K；10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone	Resolution 1.95 Å R-free 0.256
9GIC NMDA bound to compound 345 Deposited 2024-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 394–544（151 aa） Chain A 663–801（139 aa）	Not recorded	A1ILQ (2~{R})-2-azanyl-3-[[3-(phenylmethyl)-2~{H}-thiophen-5-yl]carbonylamino]propanoic acid × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；282.15 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.7 and 0.2 M lithium sulfate	Resolution 1.82 Å R-free 0.221
9GID NMDA bound to compound 338 Deposited 2024-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 394–544（151 aa） Chain A 663–801（139 aa）	Not recorded	A1ILT (2~{R})-2-azanyl-3-[(7-bromanyl-4-fluoranyl-3~{H}-1-benzothiophen-2-yl)carbonylamino]propanoic acid × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；282.15 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.7 and 0.2 M lithium sulfate	Resolution 2.00 Å R-free 0.260
9GIE NMDA bound to compound 315 Deposited 2024-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 394–544（151 aa） Chain A 663–801（139 aa） Chain B 394–544（151 aa） Chain B 663–801（139 aa）	Not recorded	A1ILS (2~{R})-2-azanyl-3-[[4-(2-ethylphenyl)-2,3-dihydro-1~{H}-indol-2-yl]carbonylamino]propanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；282.15 K；24% PEG 3350 and 0.1 M hepes pH 7.5	Resolution 2.36 Å R-free 0.260
9GIF NMDA bound to compound 288 Deposited 2024-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 394–544（151 aa） Chain A 663–801（139 aa）	Not recorded	A1ILR (2~{R})-2-azanyl-3-(2~{H}-thiophen-5-ylcarbonylamino)propanoic acid × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；282.15 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.7 and 0.2 M lithium sulfate	Resolution 1.90 Å R-free 0.214
9GIG NMDA bound to compound 387 Deposited 2024-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 394–544（151 aa） Chain B 663–800（138 aa）	Not recorded	GLU GLUTAMIC ACID × 1 A1ILO (2~{R})-2-azanyl-3-[[3-(5-ethyl-3-methyl-1,2-oxazol-4-yl)-5-fluoranyl-phenyl]carbonylamino]propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；282.15 K；10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone	Resolution 2.09 Å R-free 0.257
9GJ1 NMDA bound to compound 339 Deposited 2024-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 394–544（151 aa） Chain B 663–800（138 aa）	Not recorded	GLU GLUTAMIC ACID × 1 GOL GLYCEROL × 1 A1IME (2~{R})-2-azanyl-3-[(7-methylthieno[3,2-b]pyridin-2-yl)carbonylamino]propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；282.15 K；10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone	Resolution 1.62 Å R-free 0.230
9IYP Structure of the human GluN1-N2B NMDA receptors in the Mg2+ bound state Deposited 2024-07-31	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 27–840（814 aa） Chain C 27–840（814 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
9IYQ Structure of the human GluN1-N2B NMDA receptors in the Mg2+ free state Deposited 2024-07-31	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–847（847 aa） Chain C 1–847（847 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9MUL Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 1, Glycine and Glutamate Deposited 2025-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 394–544（151 aa） Chain A 663–800（138 aa）	Not recorded	GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 A1BRA 5-[(3-chlorobenzene-1-sulfonyl)methoxy]-6-methyl-N-[(pyridin-3-yl)methyl]pyrazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M Hepes pH 7.0, 0.2M ammonium acetate, 20% PEG-3350	Resolution 2.40 Å R-free 0.252
9MUM Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11, Glycine and Glutamate Deposited 2025-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 394–544（151 aa） Chain A 663–800（138 aa）	Not recorded	GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 A1BRB 5-[2-(3-chlorophenyl)-2,2-difluoroethoxy]-N-[1-(pyrazin-2-yl)cyclopropyl]pyrazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M Hepes pH 7.0, 0.2M ammonium acetate, 20% PEG-3350	Resolution 1.97 Å R-free 0.241
9OOQ Closed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR Deposited 2025-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 18–847（830 aa） Chain C 18–847（830 aa）	Mutation：C22S,R844N,R845G,K846A Mutation：C22S,R844N,R845G,K846A	GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 GLU GLUTAMIC ACID × 2 A1CE1 24S-hydroxycholesterol × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9OOR Open state Gly/Glu/24S-HC bound hGluN1a-2B NMDAR Deposited 2025-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 18–847（830 aa） Chain C 18–847（830 aa）	Mutation：C22S,R844N,R845G,K846A Mutation：C22S,R844N,R845G,K846A	GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 GLU GLUTAMIC ACID × 2 A1CE1 24S-hydroxycholesterol × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9OOS Non-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR Deposited 2025-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 18–847（830 aa） Chain C 18–847（830 aa）	Mutation：C22S,R844N,R845G,K846A Mutation：C22S,R844N,R845G,K846A	GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 GLU GLUTAMIC ACID × 2 A8W Pregnenolone sulfate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
9OOT Pre-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR Deposited 2025-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 18–847（830 aa） Chain C 18–847（830 aa）	Mutation：C22S,R844N,R845G,K846A Mutation：C22S,R844N,R845G,K846A	GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 GLU GLUTAMIC ACID × 2 A8W Pregnenolone sulfate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9PQH NMR Structure of Ca2+/Calmodulin bound to the GluN1 C0 domain of the NMDA receptor Deposited 2025-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–938（938 aa）	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.0 mM GluN1 C0, 1 mM Calcium chloride, 20 mM [U-99% 2H] TRIS, 93 % H2O, 7 % [U-2H] D2O, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.0 mM GluN1 C0, 1 mM Calcium chloride, 20 mM [U-99% 2H] TRIS, 100 % [U-2H] D2O, 100% D2O \| 100% D2O	Resolution not provided

83 other PDB entries and 86 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NMDZ1_HUMAN
Isoform	Q05586-6
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–868； UniProt 1–868 Author chain C； PDBConstruct 1–868； UniProt 1–868

Glutamate receptor ionotropic, NMDA 2D

Homo sapiens

UniProt O15399

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–879 Chain D； UniProt 1–879	Not recorded	Isoform 6 of Glutamate receptor ionotropic, NMDA 1 × 2 （Q05586） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 A1LW8 (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-methyl-4-[(1~{R},2~{R},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{R})-7,9,13,18-tetramethyl-16-oxidanyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-yl]butoxy]oxane-3,4,5-triol × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.20 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8Y1V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7YFF Structure of GluN1a-GluN2D NMDA receptor in complex with agonist glycine and competitive antagonist CPP. Deposited 2022-07-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–879（879 aa） Chain D 1–879（879 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 GLY GLYCINE × 2 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 3.60 Å
7YFL Structure of GluN1a-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Deposited 2022-07-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–879（879 aa） Chain D 1–879（879 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 3.90 Å
7YFM Structure of GluN1b-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Deposited 2022-07-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–879（879 aa） Chain D 1–879（879 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 5.10 Å
7YFO Structure of GluN1a E698C-GluN2D NMDA receptor in cystines crosslinked state. Deposited 2022-07-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–879（879 aa） Chain D 1–879（879 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 6.40 Å
7YFR Structure of GluN1a E698C-GluN2D NMDA receptor in cystines non-crosslinked state. Deposited 2022-07-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–879（879 aa） Chain D 1–879（879 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging	Resolution 5.10 Å
8E96 Glycine and glutamate bound Human GluN1a-GluN2D NMDA receptor Deposited 2022-08-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 28–879（852 aa） Chain D 28–879（852 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
9D37 Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 28–880（853 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
9D38 Open state of Gly-,Glu-,EU1622-240 bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 28–880（853 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.95 Å
9D39 Gly-,PPDA- bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 28–880（853 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2JL (2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9D3A Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR (Low-res) Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 28–880（853 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.78 Å
9D3B Gly-,Glu-,(S)-DQP-997-74 bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 28–880（853 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLU GLUTAMIC ACID × 2 A1A15 4-{(3R,5S)-5-(4-chlorophenyl)-3-[4-(4-chlorophenyl)-2-oxo-1,2-dihydroquinolin-3-yl]pyrazolidin-1-yl}-3,3-difluoro-4-oxobutanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.71 Å
9D3C Gly-,Glu-,(S)-(+)-ketamine bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 28–880（853 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 GLU GLUTAMIC ACID × 2 JC9 (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NMDE4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–879； UniProt 1–879 Author chain D； PDBConstruct 1–879； UniProt 1–879

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8y1v
Deposition date deposition_date	2024-01-25
Structure title title	Structure of GluN1b-GluN2D NMDA receptor in complex with competitive antagonist R-CPP and allosteric inhibitor YY-23
Keywords keywords	ion channel, calcium permeable, glutamate receptor, neuronal expression, MEMBRANE PROTEIN, MEMBRANE PROTEIN-INHIBITOR complex; MEMBRANE PROTEIN/INHIBITOR
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	54.06 Å
Radius of gyration Rg (electron density) rg_electron	54.86 Å
Forward intensity I(0) i0	1121320000.00
Molecular weight molecular_weight	249520.0 kDa
Excluded volume excluded_volume	297780 Å³
Envelope volume envelope_volume	587880 Å³
Hydration-shell volume shell_volume	94262 Å³
Envelope diameter envelope_diameter	182.6 Å
Shell Rg shell_rg	53.89 Å
Envelope Rg envelope_rg	52.52 Å
Shape Rg shape_rg	55.21 Å
Total Rg total_rg	53.78 Å
Total atoms total_atoms	31979
Residues n_residues	2760
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	179.6 Å
Rg (real space) rg_real	54.06 Å
Rg uncertainty (real space) rg_real_error	1.63 Å
I(0) (real space) i0_real	1.1210e+09
I(0) uncertainty (real space) i0_real_error	2.2180e+07
Rg (reciprocal space) rg_reciprocal	54.05 Å
I(0) (reciprocal space) i0_reciprocal	1121000000.0000
Solution quality estimate total_estimate	0.8548
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	68.1 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.269
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	93320000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.492

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Isoform 6 of Glutamate receptor ionotropic, NMDA 1
Molecular weight formula_weight	97777.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	31979

MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKSKKRNYENLDQLSYDNKRGPKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Glutamate receptor ionotropic, NMDA 2D
Molecular weight formula_weight	99057.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MRGAGGPRGPRGPAKMLLLLALACASPFPEEAPGPGGAGGPGGGLGGARPLNVALVFSGPAYAAEAARLGPAVAAAVRSPGLDVRPVALVLNGSDPRSLVLQLCDLLSGLRVHGVVFEDDSRAPAVAPILDFLSAQTSLPIVAVHGGAALVLTPKEKGSTFLQLGSSTEQQLQVIFEVLEEYDWTSFVAVTTRAPGHRAFLSYIEVLTDGSLVGWEHRGALTLDPGAGEAVLSAQLRSVSAQIRLLFCAREEAEPVFRAAEEAGLTGSGYVWFMVGPQLAGGGGSGAPGEPPLLPGGAPLPAGLFAVRSAGWRDDLARRVAAGVAVVARGAQALLRDYGFLPELGHDCRAQNRTHRGESLHRYFMNITWDNRDYSFNEDGFLVNPSLVVISLTRDRTWEVVGSWEQQTLRLKYPLWSRYGRFLQPVDDTQHLTVATLEERPFVIVEPADPISGTCIRDSVPCRSQLNRTHSPPPDAPRPEKRCCKGFCIDILKRLAHTIGFSYDLYLVTNGKHGKKIDGVWNGMIGEVFYQRADMAIGSLTINEERSEIVDFSVPFVETGISVMVARSNGTVSPSAFLEPYSPAVWVMMFVMCLTVVAVTVFIFEYLSPVGYNRSLATGKRPGGSTFTIGKSIWLLWALVFNNSVPVENPRGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYVDTVSGLSDRKFQRPQEQYPPLKFGTVPNGSTEKNIRSNYPDMHSYMVRYNQPRVEEALTQLKAGKLDAFIYDAAVLNYMARKDEGCKLVTIGSGKVFATTGYGIALHKGSRWKRPIDLALLQFLGDDEIEMLERLWLSGICHNDKIEVMSSKLDIDNMAGVFYMLLVAMGLSLLVFAWEHLVYWRLRHCLGPAASAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	;(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-methyl-4-[(1~{R},2~{R},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{R})-7,9,13,18-tetramethyl-16-oxidanyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-yl]butoxy]oxane-3,4,5-triol ;
Molecular weight formula_weight	592.8 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	82019

fit	/app/data/saxs_computation/y1/8y1v/8y1v.fit
pddf	/app/data/pr_computation/y1/8y1v/8y1v.pr.out
profile	/app/data/saxs_computation/y1/8y1v/8y1v.dat

Structure of GluN1b-GluN2D NMDA receptor in complex with competitive antagonist R-CPP and allosteric inhibitor YY-23

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 6 of Glutamate receptor ionotropic, NMDA 1

State in the Current Structure

Other States of the Same Protein in the Database

Glutamate receptor ionotropic, NMDA 2D

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)