5ewl

CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH MK-22

Method: X-RAY DIFFRACTION D_max: 133.4 Å Quality: GOOD

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

NMDA glutamate receptor subunit

Xenopus laevis

UniProt Q91977

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 23–408	Fragment：Amino Terminal Domain (UNP residues 23-408) Mutation：N61Q,N371Q	Glutamate receptor ionotropic, NMDA 2B × 1 （Q13224） ;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 NA SODIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 5SL ~{N}-[(1~{S},3~{S})-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]cyclopentyl]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.98 Å R-free 0.217
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 23–408	Fragment：Amino Terminal Domain (UNP residues 23-408) Mutation：N61Q,N371Q	Glutamate receptor ionotropic, NMDA 2B × 1 （Q13224） NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 5SL ~{N}-[(1~{S},3~{S})-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]cyclopentyl]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.98 Å R-free 0.217

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 5EWL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QEK Crystal structure of amino terminal domain of the NMDA receptor subunit GluN1 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 Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–405（383 aa） Fragment：Amino Terminal Domain, residues 23-405	Mutation：N61Q, N371Q Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；20% PEG3350, 150mM KNO3, 50mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.226
3QEK Crystal structure of amino terminal domain of the NMDA receptor subunit GluN1 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 monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–405（383 aa） Fragment：Amino Terminal Domain, residues 23-405	Mutation：N61Q, N371Q Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；20% PEG3350, 150mM KNO3, 50mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.226
3QEK Crystal structure of amino terminal domain of the NMDA receptor subunit GluN1 Deposited 2011-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–405（383 aa） Fragment：Amino Terminal Domain, residues 23-405 Chain B 23–405（383 aa） Fragment：Amino Terminal Domain, residues 23-405	Mutation：N61Q, N371Q Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N61Q, N371Q Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；20% PEG3350, 150mM KNO3, 50mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.226
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 A 23–405（383 aa） Fragment：Amino Terminal Domain, residues 23-405	Mutation：N61Q, N371Q	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 C 23–405（383 aa） Fragment：Amino Terminal Domain, residues 23-405	Mutation：N61Q, N371Q	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–405（383 aa） Fragment：Amino Terminal Domain, residues 23-405	Mutation：N61Q, N371Q	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–405（383 aa） Fragment：Amino Terminal Domain, residues 23-405	Mutation：N61Q, N371Q	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
5B3J Activation of NMDA receptors and the mechanism of inhibition by ifenprodil Deposited 2016-03-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–405（383 aa） Fragment：UNP residues 23-405	Mutation：N61Q, N371Q	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–405（383 aa） Fragment：UNP residues 23-405	Mutation：N61Q, N371Q	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
5EWJ CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL Deposited 2015-11-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–408（386 aa） Fragment：Amino Terminal Domain (UNP residues 23-408)	Mutation：N61Q,N371Q	NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.77 Å R-free 0.211
5EWJ CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL Deposited 2015-11-20	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–408（386 aa） Fragment：Amino Terminal Domain (UNP residues 23-408)	Mutation：N61Q,N371Q	NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.77 Å R-free 0.211
5EWM CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH EVT-101 Deposited 2015-11-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–408（386 aa） Fragment：Amino Terminal Domain (UNP residues 23-408)	Mutation：N61Q,N371Q	NA SODIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 5SM 5-[3-[bis(fluoranyl)methyl]-4-fluoranyl-phenyl]-3-[(2-methylimidazol-1-yl)methyl]pyridazine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.76 Å R-free 0.211
5EWM CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH EVT-101 Deposited 2015-11-20	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–408（386 aa） Fragment：Amino Terminal Domain (UNP residues 23-408)	Mutation：N61Q,N371Q	NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 5SM 5-[3-[bis(fluoranyl)methyl]-4-fluoranyl-phenyl]-3-[(2-methylimidazol-1-yl)methyl]pyridazine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.76 Å R-free 0.211
5TPW Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at the GluN2A 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 × 4 PDB declaration: tetrameric	Chain A 24–408（385 aa） Fragment：residues 24-408	Mutation：N38Q, N348Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 6 GOL GLYCEROL × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.8M Ammonium sulfate 2.5% Isopropanol	Resolution 2.91 Å R-free 0.245
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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–405（383 aa） Fragment：residues 23-405	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
5TQ0 Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in the presence of EDTA 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 × 4 PDB declaration: tetrameric	Chain A 24–408（385 aa） Fragment：residues 24-408	Mutation：N38Q, N348Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 12 IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.8 M Ammonium sulfate, 2.5% Isopropanol	Resolution 2.70 Å R-free 0.246
5TQ2 Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at GluN1 and GluN2A 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 × 4 PDB declaration: tetrameric	Chain A 24–408（385 aa） Fragment：residues 24-408	Mutation：N38Q, N348Q	ZN ZINC ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.8M Ammonium sulfate, 2.5% Isopropanol	Resolution 3.29 Å R-free 0.261

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q91977_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–386； UniProt 23–408 Author chain C； PDBConstruct 1–386； UniProt 23–408

Glutamate receptor ionotropic, NMDA 2B

Homo sapiens

UniProt Q13224

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 31–394	Fragment：Amino Terminal Domain (UNP residues 31-394) Mutation：N348D	NMDA glutamate receptor subunit × 1 （Q91977） ;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 NA SODIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 5SL ~{N}-[(1~{S},3~{S})-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]cyclopentyl]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.98 Å R-free 0.217
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 31–394	Fragment：Amino Terminal Domain (UNP residues 31-394) Mutation：N348D	NMDA glutamate receptor subunit × 1 （Q91977） NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 5SL ~{N}-[(1~{S},3~{S})-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]cyclopentyl]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.98 Å R-free 0.217

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5EWL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10EX SK5A-Matured apo state in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 59–845（787 aa） Chain D 59–845（787 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å
10EY SK5B-Matured in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
10EZ SK3D-Germline in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.76 Å
10FD SK5G-Matured in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
10FE OX1-Germline in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.55 Å
10FF SK5A-Matured glycine/glutamate in complex with GluN1-GluN2B, full refinement Deposited 2026-01-15	Different construct Different 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.06 Å
10FL SK5G-Germline Deposited 2026-01-16	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 × 6 PDB declaration: hexameric	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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.81 Å
10FN SK5A-Germline in complex with GluN1-GluN2B, full refinement Deposited 2026-01-16	Different construct Different 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.52 Å
10FO SK5B-Germline in complex with GluN1-GluN2B, full refinement Deposited 2026-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.46 Å
5EWJ CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL Deposited 2015-11-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 31–394（364 aa） Fragment：Amino Terminal Domain (UNP residues 31-394)	Mutation：N348D	NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.77 Å R-free 0.211
5EWJ CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL Deposited 2015-11-20	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 31–394（364 aa） Fragment：Amino Terminal Domain (UNP residues 31-394)	Mutation：N348D	NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.77 Å R-free 0.211
5EWM CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH EVT-101 Deposited 2015-11-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 31–394（364 aa） Fragment：Amino Terminal Domain (UNP residues 31-394)	Mutation：N348D	NA SODIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 5SM 5-[3-[bis(fluoranyl)methyl]-4-fluoranyl-phenyl]-3-[(2-methylimidazol-1-yl)methyl]pyridazine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.76 Å R-free 0.211
5EWM CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH EVT-101 Deposited 2015-11-20	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 31–394（364 aa） Fragment：Amino Terminal Domain (UNP residues 31-394)	Mutation：N348D	NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 5SM 5-[3-[bis(fluoranyl)methyl]-4-fluoranyl-phenyl]-3-[(2-methylimidazol-1-yl)methyl]pyridazine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.6M Na Formate, 0.1 M Hepes pH 7.0	Resolution 2.76 Å R-free 0.211
7EU8 Structure of the human GluN1-GluN2B NMDA receptor in complex with S-ketamine,glycine and glutamate Deposited 2021-05-16	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 1–842（842 aa） Chain D 1–842（842 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 JC9 (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.07 Å
7KL0 Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) Deposited 2020-10-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1289–1310（22 aa）	Mutation：S1303D	UZD methyl 6-O-(heptylcarbamoyl)-beta-L-altropyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 6000, 19mM HECAMEG	Resolution 2.40 Å R-free 0.258
7KL0 Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) Deposited 2020-10-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1289–1310（22 aa）	Mutation：S1303D	UZD methyl 6-O-(heptylcarbamoyl)-beta-L-altropyranoside × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 6000, 19mM HECAMEG	Resolution 2.40 Å R-free 0.258
7KL1 Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) Deposited 2020-10-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1289–1310（22 aa）	Mutation：S1303D	EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 6000, 19mM HECAMEG	Resolution 2.40 Å R-free 0.258
7KL1 Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) Deposited 2020-10-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1289–1310（22 aa）	Mutation：S1303D	EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 6000, 19mM HECAMEG	Resolution 2.40 Å R-free 0.258
7KL2 Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) Deposited 2020-10-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1289–1310（22 aa）	Mutation：S1303D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.15 M DL-Malic acid pH 7, 20% PEG 3350	Resolution 2.56 Å R-free 0.293
7UIS Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) Deposited 2022-03-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1289–1310（22 aa）	Mutation：S1303D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M Bis-tris propane pH 6.5, 0.2 M Sodium chloride, 25% PEG 3350	Resolution 2.58 Å R-free 0.268
7UJP Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B Deposited 2022-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1289–1310（22 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1 M Bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane, 0.1 M Ammonium sulfate, 25% PEG 3350, 19mM Methyl 6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside	Resolution 2.56 Å R-free 0.281
7UJP Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B Deposited 2022-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1289–1310（22 aa）	Not recorded	MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1 M Bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane, 0.1 M Ammonium sulfate, 25% PEG 3350, 19mM Methyl 6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside	Resolution 2.56 Å R-free 0.281
7UJQ Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B Deposited 2022-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1289–1310（22 aa）	Not recorded	UZD methyl 6-O-(heptylcarbamoyl)-beta-L-altropyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1 M Bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane, 0.1 M Ammonium sulfate, 25% PEG 3350, 19mM Methyl 6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside	Resolution 2.25 Å R-free 0.271
7UJQ Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B Deposited 2022-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1289–1310（22 aa）	Not recorded	UZD methyl 6-O-(heptylcarbamoyl)-beta-L-altropyranoside × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1 M Bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane, 0.1 M Ammonium sulfate, 25% PEG 3350, 19mM Methyl 6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside	Resolution 2.25 Å R-free 0.271
7UJR Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B Deposited 2022-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1289–1310（22 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 3350, 5% Ethanol	Resolution 1.95 Å R-free 0.252
7UJS Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B in complex with ADP Deposited 2022-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1289–1310（22 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 3350	Resolution 2.75 Å R-free 0.262
7UJT Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) in complex with ATP Deposited 2022-03-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1289–1310（22 aa）	Mutation：S1303D	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.2 M Sodium chloride, 25% PEG 3350	Resolution 2.10 Å R-free 0.246
8VUU Human GluN1-2B with Fab 007-168 Deposited 2024-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 31–845（815 aa） Chain D 31–845（815 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.05 Å
8VUV Human GluN1-2B with Fab 007-168 Local refinement of ATD Deposited 2024-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 31–387（357 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å
9D37 Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa）	Mutation：C838S, C849S, C588S	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
9D38 Open state of Gly-,Glu-,EU1622-240 bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa）	Mutation：C588S, C838S, C849S	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.95 Å
9D39 Gly-,PPDA- bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa）	Mutation：C588S, C838S, C849S	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2JL (2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9D3A Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR (Low-res) Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa）	Mutation：C838S, C849S	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GLU GLUTAMIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.78 Å
9D3B Gly-,Glu-,(S)-DQP-997-74 bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa）	Mutation：C588S, C838S, C849S	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLU GLUTAMIC ACID × 2 A1A15 4-{(3R,5S)-5-(4-chlorophenyl)-3-[4-(4-chlorophenyl)-2-oxo-1,2-dihydroquinolin-3-yl]pyrazolidin-1-yl}-3,3-difluoro-4-oxobutanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.71 Å
9D3C Gly-,Glu-,(S)-(+)-ketamine bound GluN1a-2B-2D NMDAR Deposited 2024-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa）	Mutation：S588C, C838S, C849S	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 GLU GLUTAMIC ACID × 2 JC9 (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
9IYP Structure of the human GluN1-N2B NMDA receptors in the Mg2+ bound state Deposited 2024-07-31	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 35–842（808 aa） Chain D 35–842（808 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
9IYQ Structure of the human GluN1-N2B NMDA receptors in the Mg2+ free state Deposited 2024-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–842（842 aa） Chain D 1–842（842 aa）	Not recorded	GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9OOQ Closed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR Deposited 2025-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Mutation：C588S,C838S,C849S Mutation：C588S,C838S,C849S	GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 GLU GLUTAMIC ACID × 2 A1CE1 24S-hydroxycholesterol × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9OOR Open state Gly/Glu/24S-HC bound hGluN1a-2B NMDAR Deposited 2025-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Mutation：C588S,C838S,C849S Mutation：C588S,C838S,C849S	GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 GLU GLUTAMIC ACID × 2 A1CE1 24S-hydroxycholesterol × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9OOS Non-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR Deposited 2025-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Mutation：C588S,C838S,C849S Mutation：C588S,C838S,C849S	GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 GLU GLUTAMIC ACID × 2 A8W Pregnenolone sulfate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
9OOT Pre-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR Deposited 2025-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–852（826 aa） Chain D 27–852（826 aa）	Mutation：C588S,C838S,C849S Mutation：C588S,C838S,C849S	GLY GLYCINE × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 GLU GLUTAMIC ACID × 2 A8W Pregnenolone sulfate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å

35 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NMDE2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–364； UniProt 31–394 Author chain D； PDBConstruct 1–364； UniProt 31–394

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	5ewl
Deposition date deposition_date	2015-11-20
Structure title title	CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH MK-22
Keywords keywords	NMDA Receptor, allosteric inhibition, GluN2B subunit, 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	41.36 Å
Radius of gyration Rg (electron density) rg_electron	41.18 Å
Forward intensity I(0) i0	359357000.00
Molecular weight molecular_weight	159330.0 kDa
Excluded volume excluded_volume	200850 Å³
Envelope volume envelope_volume	266200 Å³
Hydration-shell volume shell_volume	54418 Å³
Envelope diameter envelope_diameter	136.0 Å
Shell Rg shell_rg	46.25 Å
Envelope Rg envelope_rg	40.43 Å
Shape Rg shape_rg	41.20 Å
Total Rg total_rg	41.35 Å
Total atoms total_atoms	11224
Residues n_residues	1420
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	133.4 Å
Rg (real space) rg_real	41.36 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	3.5940e+08
I(0) uncertainty (real space) i0_real_error	6.4870e+06
Rg (reciprocal space) rg_reciprocal	41.36 Å
I(0) (reciprocal space) i0_reciprocal	359400000.0000
Solution quality estimate total_estimate	0.8977
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	0.255
Kurtosis Kurtosis kurtosis	-0.700
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39380000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.937

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	NMDA glutamate receptor subunit
Molecular weight formula_weight	43758.0 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	11493

DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLSYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGETELVPR

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Glutamate receptor ionotropic, NMDA 2B
Molecular weight formula_weight	41351.9 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

SPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRM

来源 Source

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

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 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

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	6

Entity 6 Entity 6 non-polymer

Description description	~{N}-[(1~{S},3~{S})-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]cyclopentyl]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine
Molecular weight formula_weight	375.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	269

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5ewlA01
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	5ewlA02
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	5ewlB01
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	5ewlB02
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	5ewlC01
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	5ewlC02
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	5ewlD01
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	5ewlD02
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	268.880 Å
Unit-cell length b length_b	59.940 Å
Unit-cell length c length_c	144.450 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.51 °
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	2.980 Å
Low-resolution limit resolution_low	30.040 Å
R factor r_factor	0.1644
R_work r_work	0.1618
R_free r_free	0.2166

fit	/app/data/saxs_computation/ew/5ewl/5ewl.fit
pddf	/app/data/pr_computation/ew/5ewl/5ewl.pr.out
profile	/app/data/saxs_computation/ew/5ewl/5ewl.dat

CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH MK-22

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

NMDA glutamate receptor subunit

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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 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)