Glutamate receptor ionotropic, NMDA 1
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count | Chain A； UniProt 27–841 Chain C； UniProt 26–841 | Not recorded | Glutamate receptor ionotropic, NMDA 2A × 2 （Q12879） 003-102 Heavy × 2 003-102 Light × 2 | ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE | Resolution 4.42 Å |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 8VUH | 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 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 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 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 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 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 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 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 experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–841（841 aa）
Chain C
1–841（841 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.46 Å |
| 2HQW Crystal Structure of Ca2+/Calmodulin bound to NMDA Receptor NR1C1 peptide Deposited 2006-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
875–898（24 aa）
Fragment：C-TERMINAL TAIL, C1 REGION
|
Not recorded | CA CALCIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；277.15 K；7% PEG 6000, 5mM CaCl2, 100 mM sodium acetate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.90 Å R-free 0.248 |
| 2NR1 TRANSMEMBRANE SEGMENT 2 OF NMDA RECEPTOR NR1, NMR, 10 STRUCTURES Deposited 1997-12-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
599–621（23 aa）
Fragment：TRANSMEMBRANE SEGMENT 2
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5.5；303 K
|
Resolution not provided |
| 3BYA Structure of a Calmodulin Complex Deposited 2008-01-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
875–898（24 aa）
|
Not recorded | CA CALCIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；17-19% PEG 3350, 0.120mM Ammonium Phosphate, 15% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.85 Å R-free 0.232 |
| 5H8F Structure of the apo human GluN1/GluN2A LBD Deposited 2015-12-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
394–544（151 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
Chain B
663–800（138 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
|
Not recorded | GOL GLYCEROL × 6 GLU GLUTAMIC ACID × 1 GLY GLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)
|
Resolution 1.81 Å R-free 0.207 |
| 5H8H Structure of the human GluN1/GluN2A LBD in complex with GNE3419 Deposited 2015-12-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
415–565（151 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
Chain B
684–821（138 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
|
Not recorded | ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 CA CALCIUM ION × 1 GLY GLYCINE × 1 5YC 7-[[ethyl(phenyl)amino]methyl]-2-methyl-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)
|
Resolution 2.23 Å R-free 0.227 |
| 5H8N Structure of the human GluN1/GluN2A LBD in complex with NAM Deposited 2015-12-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
394–544（151 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
Chain B
663–800（138 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
|
Not recorded | GLU GLUTAMIC ACID × 1 5YD 4-[[(4-fluorophenyl)sulfonylamino]methyl]-~{N}-(pyridin-3-ylmethyl)benzamide × 1 CA CALCIUM ION × 1 GLY GLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)
|
Resolution 2.50 Å R-free 0.236 |
| 5H8Q Structure of the human GluN1/GluN2A LBD in complex with GNE8324 Deposited 2015-12-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
394–544（151 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
Chain B
663–800（138 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
|
Not recorded | ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 GLY GLYCINE × 1 5YE 6-[[ethyl-(4-fluorophenyl)amino]methyl]-2,3-dihydro-1~{H}-cyclopenta[3,4][1,3]thiazolo[1,4-~{a}]pyrimidin-8-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)
|
Resolution 1.90 Å R-free 0.209 |
| 5I2K Structure of the human GluN1/GluN2A LBD in complex with 7-{[ethyl(4-fluorophenyl)amino]methyl}-N,2-dimethyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide (compound 19) Deposited 2016-02-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
415–565（151 aa）
Fragment：UNP residues 415-565, GT linker, UNP residues 684-821
Chain B
684–821（138 aa）
Fragment：UNP residues 415-565, GT linker, UNP residues 684-821
|
Not recorded | GLU GLUTAMIC ACID × 1 GLY GLYCINE × 1 67H 7-{[ethyl(4-fluorophenyl)amino]methyl}-N,2-dimethyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)
|
Resolution 2.86 Å R-free 0.256 |
| 5I2N Structure of the human GluN1/GluN2A LBD in complex with N-ethyl-7-{[2-fluoro-3-(trifluoromethyl)phenyl]methyl}-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide (compound 29) Deposited 2016-02-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
415–565（151 aa）
Fragment：UNP residues 415-565, GT linker, UNP residues 684-821
Chain B
684–821（138 aa）
Fragment：UNP residues 415-565, GT linker, UNP residues 684-821
|
Not recorded | CA CALCIUM ION × 1 GLU GLUTAMIC ACID × 1 67J N-ethyl-7-{[2-fluoro-3-(trifluoromethyl)phenyl]methyl}-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GLY GLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)
|
Resolution 2.12 Å R-free 0.223 |
| 5KCJ Structure of the human GluN1/GluN2A LBD in complex with GNE6901 Deposited 2016-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
415–565（151 aa）
Fragment：Ligand binding domain (UNP residues 415-565, GT linker, UNP residues 684-821)
Chain B
684–821（138 aa）
Fragment：Ligand binding domain (UNP residues 415-565, GT linker, UNP residues 684-821)
|
Not recorded | ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 GLY GLYCINE × 1 6RM 7-[(4-fluoranylphenoxy)methyl]-3-[(1~{R},2~{R})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate
|
Resolution 2.09 Å R-free 0.225 |
| 5KDT Structure of the human GluN1/GluN2A LBD in complex with GNE0723 Deposited 2016-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
415–565（151 aa）
Fragment：Ligand binding domain (UNP residues 415-565, GT linker, UNP residues 684-821)
Chain B
684–821（138 aa）
Fragment：Ligand binding domain (UNP residues 415-565, GT linker, UNP residues 684-821)
|
Not recorded | ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 6RV (1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl)pyrazol-1-yl]methyl]-5-oxidanylidene-2-(trifluoromethyl)-[1,3]thiazolo[3,2-a]pyrimidin-3-yl]cyclopropane-1-carbonitrile × 1 GLY GLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate
|
Resolution 2.44 Å R-free 0.240 |
| 5TP9 Structure of the human GluN1/GluN2A LBD in complex with compound 2 (GNE9178) Deposited 2016-10-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
415–565（151 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
Chain B
684–821（138 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
|
Not recorded | ACT ACETATE ION × 1 GLU GLUTAMIC ACID × 1 7H0 7-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-N-ethyl-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide × 1 CA CALCIUM ION × 1 GLY GLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate
|
Resolution 2.40 Å R-free 0.237 |
| 5TPA Structure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500) Deposited 2016-10-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
415–565（151 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
Chain B
684–821（138 aa）
Fragment：UNP residues 394-544, GT linker, UNP residues 663-800
|
Not recorded | GLU GLUTAMIC ACID × 1 7H2 (1R,2R)-2-(2-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-6-yl)cyclopropane-1-carbonitrile × 1 GLY GLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate
|
Resolution 2.48 Å R-free 0.241 |
| 6IRA Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 7.8 Deposited 2018-11-12 | Different construct Different mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–840（840 aa）
Chain C
1–840（840 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 GLY GLYCINE × 2 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 3 seconds before plunging
|
Resolution 3.60 Å |
| 7YFL Structure of GluN1a-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLU GLUTAMIC ACID × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 3 seconds before plunging
|
Resolution 3.90 Å |
| 7YFM Structure of GluN1b-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Deposited 2022-07-08 | Different construct Different oligomeric state 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 experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Mutation：E698C Mutation：E698C | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 3 seconds before plunging
|
Resolution 6.40 Å |
| 7YFR Structure of GluN1a E698C-GluN2D NMDA receptor in cystines non-crosslinked state. Deposited 2022-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Mutation：E698C Mutation：E698C | GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLU GLUTAMIC ACID × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 3 seconds before plunging
|
Resolution 5.10 Å |
| 8E92 D-cycloserine and glutamate bound Human GluN1a-GluN2C NMDA receptor in intact conformation Deposited 2022-08-26 | Different construct Different oligomeric state Different ligand/ion Different 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 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 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 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 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 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 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 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 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 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 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 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 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 |
| 8VUJ Human GluN1-2A with Fab 003-102 Deposited 2024-01-29 | 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 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 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 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 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 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 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 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 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 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 experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
21–393（373 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES or HEPES, pH6.5-7.5, and 6-8 %w/v PEG20000
|
Resolution 3.50 Å R-free 0.227 |
| 8ZH7 Crystal structure of N-terminal domain of N-methyl-D-aspartate receptor subunit NR1 in complex with patient-derived antibody Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
21–393（373 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES or HEPES, pH6.5-7.5, and 6-8 %w/v PEG20000
|
Resolution 3.50 Å R-free 0.227 |
| 8ZH7 Crystal structure of N-terminal domain of N-methyl-D-aspartate receptor subunit NR1 in complex with patient-derived antibody Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
21–393（373 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES or HEPES, pH6.5-7.5, and 6-8 %w/v PEG20000
|
Resolution 3.50 Å R-free 0.227 |
| 8ZH7 Crystal structure of N-terminal domain of N-methyl-D-aspartate receptor subunit NR1 in complex with patient-derived antibody Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
21–393（373 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES or HEPES, pH6.5-7.5, and 6-8 %w/v PEG20000
|
Resolution 3.50 Å R-free 0.227 |
| 9D37 Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR Deposited 2024-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different 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 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 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 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 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 structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
23–847（825 aa）
Chain C
23–847（825 aa）
|
Mutation：R844N, R845G, K846A Mutation：R844N, R845G, K846A | GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 GLU GLUTAMIC ACID × 2 JC9 (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.96 Å |
| 9GIB NMDA bound to compound 380 Deposited 2024-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
394–544（151 aa）
Chain B
663–800（138 aa）
|
Not recorded | GOL GLYCEROL × 1 GLU GLUTAMIC ACID × 1 A1ILP (2~{R})-2-azanyl-3-[[3-(5-ethyl-1,2-oxazol-4-yl)-5-fluoranyl-phenyl]carbonylamino]propanoic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；282.15 K；10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone
|
Resolution 1.95 Å R-free 0.256 |
| 9GIC NMDA bound to compound 345 Deposited 2024-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Chain A
663–801（139 aa）
|
Not recorded | A1ILQ (2~{R})-2-azanyl-3-[[3-(phenylmethyl)-2~{H}-thiophen-5-yl]carbonylamino]propanoic acid × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；282.15 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.7 and 0.2 M lithium sulfate
|
Resolution 1.82 Å R-free 0.221 |
| 9GID NMDA bound to compound 338 Deposited 2024-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Chain A
663–801（139 aa）
|
Not recorded | A1ILT (2~{R})-2-azanyl-3-[(7-bromanyl-4-fluoranyl-3~{H}-1-benzothiophen-2-yl)carbonylamino]propanoic acid × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；282.15 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.7 and 0.2 M lithium sulfate
|
Resolution 2.00 Å R-free 0.260 |
| 9GIE NMDA bound to compound 315 Deposited 2024-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
394–544（151 aa）
Chain A
663–801（139 aa）
Chain B
394–544（151 aa）
Chain B
663–801（139 aa）
|
Not recorded | A1ILS (2~{R})-2-azanyl-3-[[4-(2-ethylphenyl)-2,3-dihydro-1~{H}-indol-2-yl]carbonylamino]propanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；282.15 K；24% PEG 3350 and 0.1 M hepes pH 7.5
|
Resolution 2.36 Å R-free 0.260 |
| 9GIF NMDA bound to compound 288 Deposited 2024-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Chain A
663–801（139 aa）
|
Not recorded | A1ILR (2~{R})-2-azanyl-3-(2~{H}-thiophen-5-ylcarbonylamino)propanoic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；282.15 K；20% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.7 and 0.2 M lithium sulfate
|
Resolution 1.90 Å R-free 0.214 |
| 9GIG NMDA bound to compound 387 Deposited 2024-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
394–544（151 aa）
Chain B
663–800（138 aa）
|
Not recorded | GLU GLUTAMIC ACID × 1 A1ILO (2~{R})-2-azanyl-3-[[3-(5-ethyl-3-methyl-1,2-oxazol-4-yl)-5-fluoranyl-phenyl]carbonylamino]propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；282.15 K；10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone
|
Resolution 2.09 Å R-free 0.257 |
| 9GJ1 NMDA bound to compound 339 Deposited 2024-08-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
394–544（151 aa）
Chain B
663–800（138 aa）
|
Not recorded | GLU GLUTAMIC ACID × 1 GOL GLYCEROL × 1 A1IME (2~{R})-2-azanyl-3-[(7-methylthieno[3,2-b]pyridin-2-yl)carbonylamino]propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；282.15 K；10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone
|
Resolution 1.62 Å R-free 0.230 |
| 9IYP Structure of the human GluN1-N2B NMDA receptors in the Mg2+ bound state Deposited 2024-07-31 | Different construct Different oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
394–544（151 aa）
Chain A
663–800（138 aa）
|
Not recorded | GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 A1BRA 5-[(3-chlorobenzene-1-sulfonyl)methoxy]-6-methyl-N-[(pyridin-3-yl)methyl]pyrazine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M Hepes pH 7.0, 0.2M ammonium acetate, 20% PEG-3350
|
Resolution 2.40 Å R-free 0.252 |
| 9MUM Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11, Glycine and Glutamate Deposited 2025-01-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
394–544（151 aa）
Chain A
663–800（138 aa）
|
Not recorded | GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 A1BRB 5-[2-(3-chlorophenyl)-2,2-difluoroethoxy]-N-[1-(pyrazin-2-yl)cyclopropyl]pyrazine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M Hepes pH 7.0, 0.2M ammonium acetate, 20% PEG-3350
|
Resolution 1.97 Å R-free 0.241 |
| 9OOQ Closed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR Deposited 2025-05-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
18–847（830 aa）
Chain C
18–847（830 aa）
|
Mutation：C22S,R844N,R845G,K846A Mutation：C22S,R844N,R845G,K846A | GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 GLU GLUTAMIC ACID × 2 A1CE1 24S-hydroxycholesterol × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9OOR Open state Gly/Glu/24S-HC bound hGluN1a-2B NMDAR Deposited 2025-05-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
18–847（830 aa）
Chain C
18–847（830 aa）
|
Mutation：C22S,R844N,R845G,K846A Mutation：C22S,R844N,R845G,K846A | GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 GLU GLUTAMIC ACID × 2 A1CE1 24S-hydroxycholesterol × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 9OOS Non-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR Deposited 2025-05-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
18–847（830 aa）
Chain C
18–847（830 aa）
|
Mutation：C22S,R844N,R845G,K846A Mutation：C22S,R844N,R845G,K846A | GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 GLU GLUTAMIC ACID × 2 A8W Pregnenolone sulfate × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 9OOT Pre-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR Deposited 2025-05-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
18–847（830 aa）
Chain C
18–847（830 aa）
|
Mutation：C22S,R844N,R845G,K846A Mutation：C22S,R844N,R845G,K846A | GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 GLU GLUTAMIC ACID × 2 A8W Pregnenolone sulfate × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.13 Å |
| 9PQH NMR Structure of Ca2+/Calmodulin bound to the GluN1 C0 domain of the NMDA receptor Deposited 2025-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–938（938 aa）
|
Not recorded | CA CALCIUM ION × 4 |
SOLUTION NMR
NMR measurement conditions
pH 7；308 K；Ionic strength (raw mmCIF value) 1；Pressure 1
NMR sample composition
0.4 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.0 mM GluN1 C0, 1 mM Calcium chloride, 20 mM [U-99% 2H] TRIS, 93 % H2O, 7 % [U-2H] D2O, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
0.4 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.0 mM GluN1 C0, 1 mM Calcium chloride, 20 mM [U-99% 2H] TRIS, 100 % [U-2H] D2O, 100% D2O | 100% D2O
|
Resolution not provided |
83 other PDB entries and 86 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | NMDZ1_HUMAN |
| Isoform | — |
| PDB entities | 1, 3 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–815； UniProt 27–841 Author chain C； PDBConstruct 1–816； UniProt 26–841 |
