6e7s

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5

Method: X-RAY DIFFRACTION D_max: 133.2 Å Quality: GOOD

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

Glutamate receptor ionotropic, NMDA 1

Xenopus laevis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–407	Fragment：Extracellular residues 23-407 Mutation：N61Q, N371Q	Glutamate receptor ionotropic, NMDA 2B × 1 （Q00960） ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 5 HZ4 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](ethyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.72 Å R-free 0.234
2	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 23–407	Fragment：Extracellular residues 23-407 Mutation：N61Q, N371Q	Glutamate receptor ionotropic, NMDA 2B × 1 （Q00960） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 3 HZ4 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](ethyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.72 Å R-free 0.234

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 6E7S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6E7R Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HYS N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.10 Å R-free 0.218
6E7R Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HYS N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.10 Å R-free 0.218
6E7T Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HYY N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.31 Å R-free 0.225
6E7T Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6 Deposited 2018-07-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 5 HYY N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.31 Å R-free 0.225
6E7U Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-31 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HX7 N-{4-[(2S)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.27 Å R-free 0.237
6E7U Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-31 Deposited 2018-07-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HX7 N-{4-[(2S)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.27 Å R-free 0.237
6E7V Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-88 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 T88 N-{4-[(2R)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.60 Å R-free 0.233
6E7V Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-88 Deposited 2018-07-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 5 T88 N-{4-[(2R)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.60 Å R-free 0.233
6E7W Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-115 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HXM N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propan-2-yl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.67 Å R-free 0.232
6E7W Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-115 Deposited 2018-07-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 5 HXM N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propan-2-yl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.67 Å R-free 0.232
6E7X Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-97 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 5 T97 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](2-methylpropyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.58 Å R-free 0.216
6E7X Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-97 Deposited 2018-07-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–407（385 aa） Fragment：Extracellular residues 23-407	Mutation：N61Q, N371Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 4 T97 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](2-methylpropyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.58 Å R-free 0.216
7TE6 Crystal structure of GluN1b-2B ATD complexed to Fab5 anti-GluN2B antibody Deposited 2022-01-04	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 23–405（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；2.1 M sodium/potassium phosphate, 100 mM lithium sulfate, 100 mM CAPS, pH 10.5, 4% formamide	Resolution 4.55 Å R-free 0.324
7TE6 Crystal structure of GluN1b-2B ATD complexed to Fab5 anti-GluN2B antibody Deposited 2022-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 23–405（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；2.1 M sodium/potassium phosphate, 100 mM lithium sulfate, 100 mM CAPS, pH 10.5, 4% formamide	Resolution 4.55 Å R-free 0.324
8G18 Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108 Deposited 2023-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–185（163 aa） Chain A 190–386（197 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 YGW N-(4-{3-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-oxopropoxy}phenyl)methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；sodium formate, HEPES, sodium chloride, Tris	Resolution 2.85 Å R-free 0.246
8G18 Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108 Deposited 2023-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–185（163 aa） Chain C 190–386（197 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 YGW N-(4-{3-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-oxopropoxy}phenyl)methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；sodium formate, HEPES, sodium chloride, Tris	Resolution 2.85 Å R-free 0.246

8 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NMDZ1_XENLA
Isoform	A0A1L8F5J9-8
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–385； UniProt 23–407 Author chain C； PDBConstruct 1–385； UniProt 23–407

Glutamate receptor ionotropic, NMDA 2B

Rattus norvegicus

UniProt Q00960

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 32–394	Fragment：Extracellular residues 32-394 Mutation：N348D	Glutamate receptor ionotropic, NMDA 1 × 1 （A0A1L8F5J9） ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 5 HZ4 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](ethyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.72 Å R-free 0.234
2	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 32–394	Fragment：Extracellular residues 32-394 Mutation：N348D	Glutamate receptor ionotropic, NMDA 1 × 1 （A0A1L8F5J9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 3 HZ4 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](ethyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.72 Å R-free 0.234

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6E7S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JPW Crystal structure of amino terminal domain of the NMDA receptor subunit NR2B Deposited 2009-09-04	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 32–394（363 aa） Fragment：Amino terminal domain	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 17 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；303 K；3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 2.80 Å R-free 0.231
3JPW Crystal structure of amino terminal domain of the NMDA receptor subunit NR2B Deposited 2009-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 32–394（363 aa） Fragment：Amino terminal domain	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CL CHLORIDE ION × 34 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；303 K；3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 2.80 Å R-free 0.231
3JPY Crystal structure of the zinc-bound amino terminal domain of the NMDA receptor subunit NR2B Deposited 2009-09-04	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 32–394（363 aa） Fragment：Amino terminal domain	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 5 NA SODIUM ION × 1 ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；303 K；3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, 0.1mM ZnCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 3.21 Å R-free 0.233
3JPY Crystal structure of the zinc-bound amino terminal domain of the NMDA receptor subunit NR2B Deposited 2009-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 32–394（363 aa） Fragment：Amino terminal domain	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CL CHLORIDE ION × 10 NA SODIUM ION × 2 ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；303 K；3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, 0.1mM ZnCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 3.21 Å R-free 0.233
3QEL Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with ifenprodil Deposited 2011-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394 Chain D 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394	Mutation：N348D Mutation：N348D	NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.60 Å R-free 0.238
3QEL Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with ifenprodil Deposited 2011-01-20	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 B 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394 Chain D 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394	Mutation：N348D Mutation：N348D	NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.60 Å R-free 0.238
3QEM Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with Ro 25-6981 Deposited 2011-01-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 QEM 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.00 Å R-free 0.250
3QEM Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with Ro 25-6981 Deposited 2011-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 1 QEM 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.00 Å R-free 0.250
4PE5 Crystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel Deposited 2014-04-22	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 B 27–852（826 aa） Fragment：UNP residues 27-852 Chain D 27–852（826 aa） Fragment：UNP residues 27-852	Mutation：S214C, N348D, D557C, C588S, I815C, C838S, C849S, del(C395), del(P396), del(E397), del(E399), del(E400), del(E402) Mutation：S214C, N348D, D557C, C588S, I815C, C838S, C849S, del(C395), del(P396), del(E397), del(E399), del(E400), del(E402)	W TUNGSTEN ION × 84 GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 2 GLU GLUTAMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；PEG 4000, Tris-HCl, NaCl, Magnesium acetate, metatungstate	Resolution 3.96 Å R-free 0.295
5B3J Activation of NMDA receptors and the mechanism of inhibition by ifenprodil Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 31–394（364 aa） Fragment：UNP residues 31-394	Mutation：N348D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；0.1M sodium acetate, 27% PEG3350, 2.2M sodium formate, 0.05 M calcium chloride	Resolution 2.90 Å R-free 0.302
5B3J Activation of NMDA receptors and the mechanism of inhibition by ifenprodil Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 31–394（364 aa） Fragment：UNP residues 31-394	Mutation：N348D	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；0.1M sodium acetate, 27% PEG3350, 2.2M sodium formate, 0.05 M calcium chloride	Resolution 2.90 Å R-free 0.302
5FXG GLUN1B-GLUN2B NMDA RECEPTOR IN ACTIVE CONFORMATION Deposited 2016-03-02	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 27–852（826 aa） Fragment：UNP RESIDUES 27-852 Chain D 27–852（826 aa） Fragment：UNP RESIDUES 27-852	Mutation：YES Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3 cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 6.80 Å
5FXH GluN1b-GluN2B NMDA receptor in non-active-1 conformation Deposited 2016-03-02	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 27–852（826 aa） Fragment：UNP RESIDUES 27-852 Chain D 27–852（826 aa） Fragment：UNP RESIDUES 27-852	Mutation：YES Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3 cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 5.00 Å
5FXI GluN1b-GluN2B NMDA receptor structure in non-active-2 conformation Deposited 2016-03-02	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 27–852（826 aa） Fragment：UNP RESIDUES 27-852 Chain D 27–852（826 aa） Fragment：UNP RESIDUES 27-852	Mutation：YES Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002 % MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002 % MNG-3 cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 6.40 Å
5FXJ GluN1b-GluN2B NMDA receptor structure-Class X Deposited 2016-03-02	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 27–852（826 aa） Fragment：ATD, LBD, TMD, UNP RESIDUES 27-852 Chain D 27–852（826 aa） Fragment：ATD, LBD, TMD, UNP RESIDUES 27-852	Mutation：YES Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3 cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 6.25 Å
5FXK GluN1b-GluN2B NMDA receptor structure-Class Y Deposited 2016-03-02	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 27–852（826 aa） Fragment：UNP RESIDUES 27-852 Chain D 27–852（826 aa） Fragment：UNP RESIDUES 27-852	Mutation：YES Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002 % MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002 % MNG-3 cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 6.40 Å
5TPZ Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in apo closed state Deposited 2016-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–393（362 aa） Fragment：residues 32-393	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；20% PEG 3350, 1.4M Sodium formate, 0.3M Sodium thyocyanate, 0.1M sodium acetate pH 5.0	Resolution 3.10 Å R-free 0.300
6CNA GluN1-GluN2B NMDA receptors with exon 5 Deposited 2018-03-07	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 B 34–843（810 aa） Fragment：residues 34-843 Chain D 34–843（810 aa） Fragment：residues 34-843	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
6E7R Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HYS N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.10 Å R-free 0.218
6E7R Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HYS N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.10 Å R-free 0.218
6E7T Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6 Deposited 2018-07-27	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–393（362 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HYY N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.31 Å R-free 0.225
6E7T Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6 Deposited 2018-07-27	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–393（362 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 5 HYY N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.31 Å R-free 0.225
6E7U Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-31 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HX7 N-{4-[(2S)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.27 Å R-free 0.237
6E7U Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-31 Deposited 2018-07-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HX7 N-{4-[(2S)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.27 Å R-free 0.237
6E7V Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-88 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 T88 N-{4-[(2R)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.60 Å R-free 0.233
6E7V Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-88 Deposited 2018-07-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 5 T88 N-{4-[(2R)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.60 Å R-free 0.233
6E7W Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-115 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HXM N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propan-2-yl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.67 Å R-free 0.232
6E7W Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-115 Deposited 2018-07-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 5 HXM N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propan-2-yl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.67 Å R-free 0.232
6E7X Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-97 Deposited 2018-07-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 5 T97 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](2-methylpropyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.58 Å R-free 0.216
6E7X Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-97 Deposited 2018-07-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394	Mutation：N348D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 4 T97 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](2-methylpropyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil	Resolution 2.58 Å R-free 0.216
6WHR GluN1b-GluN2B NMDA receptor in non-active 2 conformation at 4 angstrom resolution Deposited 2020-04-08	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.99 Å
6WHS GluN1b-GluN2B NMDA receptor in non-active 1 conformation at 3.95 angstrom resolution Deposited 2020-04-08	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 B 27–852（826 aa） Chain D 27–852（826 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 4.00 Å
6WHT GluN1b-GluN2B NMDA receptor in active conformation at 4.4 angstrom resolution Deposited 2020-04-08	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.39 Å
6WHU GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 1 Deposited 2020-04-08	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	QGM (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 QGP (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
6WHV GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 2 Deposited 2020-04-08	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 QGP (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid × 2 QGM (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.05 Å
6WI0 GluN1b-GluN2B NMDA receptor in complex with GluN1 antagonist L689,560, class 2 Deposited 2020-04-08	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	QGM (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.27 Å
7SAA Glycine and glutamate bound GluN1a-GluN2B NMDA receptors in non-active 1 conformation at 2.97 Angstrom resolution Deposited 2021-09-22	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
7SAB Phencyclidine-bound GluN1a-GluN2B NMDA receptors Deposited 2021-09-22	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 1PC 1-(PHENYL-1-CYCLOHEXYL)PIPERIDINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7SAC S-(+)-ketamine bound GluN1a-GluN2B NMDA receptors at 3.69 Angstrom resolution Deposited 2021-09-22	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å
7SAD Memantine-bound GluN1a-GluN2B NMDA receptors Deposited 2021-09-22	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 377 Memantine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
7TE6 Crystal structure of GluN1b-2B ATD complexed to Fab5 anti-GluN2B antibody Deposited 2022-01-04	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 31–394（364 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；2.1 M sodium/potassium phosphate, 100 mM lithium sulfate, 100 mM CAPS, pH 10.5, 4% formamide	Resolution 4.55 Å R-free 0.324
7TE6 Crystal structure of GluN1b-2B ATD complexed to Fab5 anti-GluN2B antibody Deposited 2022-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 31–394（364 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；2.1 M sodium/potassium phosphate, 100 mM lithium sulfate, 100 mM CAPS, pH 10.5, 4% formamide	Resolution 4.55 Å R-free 0.324
7TE9 Cryo-EM structure of GluN1b-2B NMDAR complexed to Fab2 class1 Deposited 2022-01-04	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 × 8 PDB declaration: octameric	Chain B 31–852（822 aa） Chain D 31–852（822 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
7TEB Cryo-EM structure of GluN1b-2B NMDAR complexed to Fab2 non-active1-like Deposited 2022-01-04	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 × 8 PDB declaration: octameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.23 Å
7TEE Cryo-EM structure of GluN1b-2B NMDAR complexed to Fab2 Non-active2-like Deposited 2022-01-04	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 × 8 PDB declaration: octameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.59 Å
7TEQ Cryo-EM structure of GluN1b-2B NMDAR in complex with Fab5 active conformation Deposited 2022-01-05	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 × 8 PDB declaration: octameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.51 Å
7TER Cryo-EM structure of GluN1b-2B NMDAR in complex with Fab5 non-active2 conformation Deposited 2022-01-05	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 × 8 PDB declaration: octameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.23 Å
7TES Cryo-EM structure of GluN1b-2B NMDAR in complex with Fab5 in Non-active1 conformation Deposited 2022-01-05	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 × 8 PDB declaration: octameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
7TET Cryo-EM structure of GluN1b-2B NMDAR in complex with Fab5 in non-active2-like conformation Deposited 2022-01-05	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 × 8 PDB declaration: octameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.45 Å
8G18 Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108 Deposited 2023-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–394（363 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 YGW N-(4-{3-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-oxopropoxy}phenyl)methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；sodium formate, HEPES, sodium chloride, Tris	Resolution 2.85 Å R-free 0.246
8G18 Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108 Deposited 2023-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–394（363 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 YGW N-(4-{3-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-oxopropoxy}phenyl)methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；sodium formate, HEPES, sodium chloride, Tris	Resolution 2.85 Å R-free 0.246
8VUY Rat GluN1-2B with Fab 003-102 Deposited 2024-01-30	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 × 8 PDB declaration: octameric	Chain B 34–845（812 aa） Chain D 34–845（812 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.81 Å
8VVH rat GluN1a-2B Fab 003-102 local refinement Deposited 2024-01-31	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 34–387（354 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.95 Å
8XLK Structure of native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat cortex and hippocampus Deposited 2023-12-26	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 × 12 PDB declaration: dodecameric	Chain D 1–1482（1482 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9ARE Rat GluN1-GluN2B NMDA receptor channel in complex with glycine, glutamate, and EU-1622-A, in open-channel conformation Deposited 2024-02-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
9ARF Rat GluN1-GluN2B NMDA receptor channel in complex with glycine, glutamate, and EU-1622-A, in nonactive1 conformation Deposited 2024-02-23	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9ARG Rat GluN1-GluN2B NMDA receptor channel in apo conformation Deposited 2024-02-23	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 27–852（826 aa） Chain D 27–852（826 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
9ARH Rat GluN1-GluN2B NMDA receptor channel in complex with glycine Deposited 2024-02-23	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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å
9ARI Rat GluN1-GluN2B NMDA receptor channel in complex with glutamate Deposited 2024-02-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9JNN Structure of native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex and hippocampus Deposited 2024-09-23	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 × 12 PDB declaration: dodecameric	Chain B 35–845（811 aa） Chain D 35–845（811 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.40 Å
9OBS glutamate/glycine-bound GluN1a/2B NMDAR Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9OBT TMD of glutamate/glycine-bound GluN1a/2B NMDAR Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9OBU glycine/glutamate and Mg2+-bound GluN1a/2B NMDAR Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9OBV Mg2+-bound GluN1a/2B NMDAR (upper) Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
9OBW Mg2+ bound GluN1a/2B NMDAR (lower) Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9OBX glutamate/glycine and Ca2+-bound GluN1a/2B NMDAR Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.59 Å
9OBY Ca2+-bound GluN1a/2B NMDAR (S1) Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9OBZ Ca2+-bound GluN1a/2B NMDAR (S2) Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
9OC0 Ca2+-bound GluN1a/2B NMDAR (S3) Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9OC1 Ca2+-bound GluN1a/2B NMDAR (S4) Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	CA CALCIUM ION × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å
9OC2 Ca2+-bound GluN1a/2B NMDAR (S5) Deposited 2025-04-23	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 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å
9OOU Glycine/Glutamate/EU 1622-240 rGluN1a-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 B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 A1AFT (5M)-5-(3-bromo-4-fluorophenyl)-6-ethynyl-3-[2-(3-fluoro-3-methylazetidin-1-yl)-2-oxoethyl]thieno[2,3-d]pyrimidin-4(3H)-one × 4 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å

59 other PDB entries and 72 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NMDE2_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–363； UniProt 32–394 Author chain D； PDBConstruct 1–363； UniProt 32–394

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6e7s
Deposition date deposition_date	2018-07-27
Structure title title	Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5
Keywords keywords	NMDA Receptor, Ion channel, Allosteric modulation, Extracellular domain, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	41.30 Å
Radius of gyration Rg (electron density) rg_electron	41.15 Å
Forward intensity I(0) i0	365193000.00
Molecular weight molecular_weight	159400.0 kDa
Excluded volume excluded_volume	200330 Å³
Envelope volume envelope_volume	264650 Å³
Hydration-shell volume shell_volume	54189 Å³
Envelope diameter envelope_diameter	142.7 Å
Shell Rg shell_rg	46.10 Å
Envelope Rg envelope_rg	40.37 Å
Shape Rg shape_rg	41.17 Å
Total Rg total_rg	41.31 Å
Total atoms total_atoms	11214
Residues n_residues	1441
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	133.2 Å
Rg (real space) rg_real	41.31 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	3.6520e+08
I(0) uncertainty (real space) i0_real_error	5.9970e+06
Rg (reciprocal space) rg_reciprocal	41.30 Å
I(0) (reciprocal space) i0_reciprocal	365200000.0000
Solution quality estimate total_estimate	0.8263
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.6 Å
Skewness Skewness skewness	0.263
Kurtosis Kurtosis kurtosis	-0.684
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42480000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Glutamate receptor ionotropic, NMDA 1
Molecular weight formula_weight	43162.3 kDa
Mutation mutation	N61Q, N371Q
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	11392

DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLSYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGET

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI Class编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Glutamate receptor ionotropic, NMDA 2B
Molecular weight formula_weight	41280.8 kDa
Mutation mutation	N348D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPSEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRM

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 non-polymer

Description description	N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](ethyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide
Molecular weight formula_weight	461.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	6e7sA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	6e7sA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	6e7sB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	6e7sB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	6e7sC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	6e7sC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	6e7sD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	6e7sD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

▶

8. Citations (1)

▶

Unit-cell length a length_a	268.430 Å
Unit-cell length b length_b	60.633 Å
Unit-cell length c length_c	145.391 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.720 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1909
R_work r_work	0.1887
R_free r_free	0.2343

fit	/app/data/saxs_computation/e7/6e7s/6e7s.fit
pddf	/app/data/pr_computation/e7/6e7s/6e7s.pr.out
profile	/app/data/saxs_computation/e7/6e7s/6e7s.dat

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5

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

Glutamate receptor ionotropic, NMDA 1

State in the Current Structure

Other States of the Same Protein in the Database

Glutamate receptor ionotropic, NMDA 2B

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)