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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q00960 New Search
60PDB entries
74Biological assembly
119chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3JPW Crystal structure of amino terminal domain of the NMDA receptor subunit NR2B Deposited 2009-09-04 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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
6E7S Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5 Deposited 2018-07-27 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 × 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
6E7S Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5 Deposited 2018-07-27 Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 × 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
6E7T Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6 Deposited 2018-07-27 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.