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5tpa

Structure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500)

Method: X-RAY DIFFRACTION Dmax: 86.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate receptor ionotropic, NMDA 2A

Homo sapiens

UniProt Q12879

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 401–539 Chain A； UniProt 661–802 Fragment：Ligand binding domain (UNP residues 401-539, GT linker, UNP residues 661-802) Glutamate receptor ionotropic, NMDA 1 × 1 （Q05586） 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

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 5TPA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3NFL Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit Deposited 2010-06-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1449–1464（16 aa） Fragment：UNP residues 1449-1464
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG 4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.91 Å R-free 0.246
3NFL Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit Deposited 2010-06-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1449–1464（16 aa） Fragment：UNP residues 1449-1464
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG 4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.91 Å R-free 0.246
3NFL Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit Deposited 2010-06-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1449–1464（16 aa） Fragment：UNP residues 1449-1464
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG 4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.91 Å R-free 0.246
3NFL Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit Deposited 2010-06-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1449–1464（16 aa） Fragment：UNP residues 1449-1464
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG 4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.91 Å R-free 0.246
3NFL Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit Deposited 2010-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1449–1464（16 aa） Fragment：UNP residues 1449-1464
Chain H 1449–1464（16 aa） Fragment：UNP residues 1449-1464
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG 4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.91 Å R-free 0.246
3NFL Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit Deposited 2010-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1449–1464（16 aa） Fragment：UNP residues 1449-1464
Chain G 1449–1464（16 aa） Fragment：UNP residues 1449-1464
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG 4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.91 Å R-free 0.246
5H8F Structure of the apo human GluN1/GluN2A LBD Deposited 2015-12-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–539（139 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
Chain A 661–802（142 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–539（139 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
Chain A 661–802（142 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–539（139 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
Chain A 661–802（142 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–539（139 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
Chain A 661–802（142 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–539（139 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
Chain A 661–802（142 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–539（139 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
Chain A 661–802（142 aa） Fragment：UNP residues 401-539, GT linker, UNP residues 661-802
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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–539（139 aa） Fragment：Ligand binding domain (UNP residues 401-539, GT linker, UNP residues 661-802)
Chain A 661–802（142 aa） Fragment：Ligand binding domain (UNP residues 401-539, GT linker, UNP residues 661-802)
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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–539（139 aa） Fragment：Ligand binding domain (UNP residues 401-539, GT linker, UNP residues 661-802)
Chain A 661–802（142 aa） Fragment：Ligand binding domain (UNP residues 401-539, GT linker, UNP residues 661-802)
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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 401–539（139 aa） Fragment：Ligand binding domain (UNP residues 401-539, GT linker, UNP residues 661-802)
Chain A 661–802（142 aa） Fragment：Ligand binding domain (UNP residues 401-539, GT linker, UNP residues 661-802)
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
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–842（842 aa）
Chain D 1–842（842 aa）
Mutation：E656R, E657R Mutation：E656R, E657R 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–841（841 aa）
Chain D 1–841（841 aa）
Mutation：E656R, E657R Mutation：E656R, E657R 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–841（841 aa）
Chain D 1–841（841 aa）
Mutation：E656R, E657R Mutation：E656R, E657R 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–841（841 aa）
Chain D 1–841（841 aa）
Mutation：E656R, E657R Mutation：E656R, E657R 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–842（842 aa）
Chain C 1–842（842 aa）
Mutation：L794C Mutation：L794C 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–842（842 aa）
Chain C 1–842（842 aa）
Mutation：L794C Mutation：L794C 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–842（842 aa）
Chain C 1–842（842 aa）
Mutation：L794C Mutation：L794C 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–842（842 aa）
Chain C 1–842（842 aa）
Mutation：L794C Mutation：L794C 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–842（842 aa）
Chain C 1–842（842 aa）
Mutation：L794C Mutation：L794C 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–841（841 aa）
Chain D 1–841（841 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
8E99 Human GluN1a-GluN2A-GluN2C triheteromeric NMDA receptor in complex with Nb-4 Deposited 2022-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 30–851（822 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–841（841 aa）
Chain C 1–841（841 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–841（841 aa）
Chain C 1–841（841 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–841（841 aa）
Chain C 1–841（841 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–841（841 aa）
Chain C 1–841（841 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
8VUH Human GluN1-2A IgG 003-102 splayed conformation Deposited 2024-01-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 34–841（808 aa）
Chain D 34–841（808 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 34–841（808 aa）
Chain D 34–841（808 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 34–399（366 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 34–841（808 aa）
Chain D 34–841（808 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 34–396（363 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 34–841（808 aa）
Chain D 34–841（808 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
8VUT Human GluN1-2A with IgG 008-218 Deposited 2024-01-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 34–841（808 aa）
Chain D 34–841（808 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
9MUL Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 1, Glycine and Glutamate Deposited 2025-01-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 401–539（139 aa）
Chain B 661–802（142 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 401–539（139 aa）
Chain B 661–802（142 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
9PQI NMR Structure of Ca2+/Calmodulin bound to the GluN2A C0 domain of the NMDA receptor Deposited 2025-07-22 Different construct Different mutation/modification 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 1–1464（1464 aa）
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 1；Pressure 1
NMR sample composition 400 uM [U-100% 13C; U-100% 15N] Calmodulin, 1 mM GluN2, 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 400 uM [U-100% 13C; U-100% 15N] Calmodulin, 1 mM GluN2, 1 mM Calcium chloride, 20 mM [U-99% 2H] TRIS, 100 % [U-2H] D2O, 100% D2O | 100% D2O
Resolution not provided

35 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NMDE1_HUMAN
Isoform Q12879-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–141； UniProt 401–539 Author chain A； PDBConstruct 144–285； UniProt 661–802

Glutamate receptor ionotropic, NMDA 1

Homo sapiens

UniProt Q05586

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 415–565 Chain B； UniProt 684–821 Fragment：UNP residues 394-544, GT linker, UNP residues 663-800 Glutamate receptor ionotropic, NMDA 2A × 1 （Q12879） 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

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 5TPA 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method 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）
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 oligomeric state Different ligand/ion Different experimental method 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）
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 method 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 method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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
8Y1V Structure of GluN1b-GluN2D NMDA receptor in complex with competitive antagonist R-CPP and allosteric inhibitor YY-23 Deposited 2024-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 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
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 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 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 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 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 ligand/ion 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 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 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 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 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 ligand/ion 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 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method 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）
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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 Q05586-5
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–153； UniProt 415–565 Author chain B； PDBConstruct 156–293； UniProt 684–821

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

SAXS profile for 5tpa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tpa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tpa
Deposition date deposition_date2016-10-20
Structure title titleStructure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500)
Keywords keywordsNMDA receptor, glutamate, glycine, calcium channel, membrane, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.96 Å
Radius of gyration Rg (electron density) rg_electron24.77 Å
Forward intensity I(0) i062747900.00
Molecular weight molecular_weight62298.0 kDa
Excluded volume excluded_volume78188 ų
Envelope volume envelope_volume95003 ų
Hydration-shell volume shell_volume31366 ų
Envelope diameter envelope_diameter89.0 Å
Shell Rg shell_rg32.69 Å
Envelope Rg envelope_rg25.13 Å
Shape Rg shape_rg24.75 Å
Total Rg total_rg25.72 Å
Total atoms total_atoms4376
Residues n_residues554
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax86.2 Å
Rg (real space) rg_real25.88 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real6.2750e+07
I(0) uncertainty (real space) i0_real_error8.8850e+05
Rg (reciprocal space) rg_reciprocal25.91 Å
I(0) (reciprocal space) i0_reciprocal62750000.0000
Solution quality estimate total_estimate0.8867
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.1 Å
Skewness Skewness skewness0.263
Kurtosis Kurtosis kurtosis-0.332
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13430000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5tpaa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.0 — automated matches
Domain ID domain_idd5tpab_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like

CATH v4.4 (4 domains)

Domain ID domain_id5tpaA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id5tpaA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id5tpaB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id5tpaB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
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8. Citations (1)

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9. Files and Curves (10)