← Back to search
3lmk

Ligand Binding Domain of Metabotropoc glutamate receptor mGluR5 complexed with glutamate

Method: X-RAY DIFFRACTION Dmax: 94.8 Å Quality: REASONABLE
▼

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

Metabotropic glutamate receptor 5

Homo sapiens

UniProt P41594

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 18–505 Chain B； UniProt 18–505 Fragment：Ligand binding domain Mutation：C241S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GLU GLUTAMIC ACID × 2 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；25% PEG 8000, 0.2M NaCl, 0.1M Hepes. protein concentration 5mg/mL plus 5mM L-Glu. Cryoprotectant used: 33% PEG 8000, 0.2M NaCl and 0.1M Hepes plus 20% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.44 Å R-free 0.281

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 3LMK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4OO9 Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator mavoglurant Deposited 2014-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 569–678（110 aa） Fragment：SEE REMARK 999
Chain A 680–836（157 aa） Fragment：SEE REMARK 999
Mutation：yes Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：yes Non-standard monomer：Yes (specific site not provided by mmCIF) OLA OLEIC ACID × 4 2U8 Mavoglurant × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.8；293.1 K；24-34% v/v PEG400, 0.2 M ammonium phosphate dibasic, 0.1 M MES, pH 6.8, LIPIDIC CUBIC PHASE, temperature 293.1K
Resolution 2.60 Å R-free 0.275
5CGC Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator 3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-yl)pyrimidin-4-yl]benzonitrile Deposited 2015-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 569–678（110 aa）
Chain A 679–836（158 aa）
Mutation：;E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A ; Mutation：;E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A ; OLA OLEIC ACID × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 51D 3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-yl)pyrimidin-4-yl]benzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.8；293.1 K；24-34% V/V PEG400, 0.2 M AMMONIUM PHOSPHATE DIBASIC, 0.1 M MES, PH 6.8,
Resolution 3.10 Å R-free 0.287
5CGD Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile - (HTL14242) Deposited 2015-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 569–678（110 aa）
Chain A 679–836（158 aa）
Mutation：;E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A ; Mutation：;E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A ; OLA OLEIC ACID × 4 51E 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.8；293.1 K；24-34% V/V PEG400, 0.2 M AMMONIUM PHOSPHATE DIBASIC, 0.1 M MES, PH 6.8,
Resolution 2.60 Å R-free 0.285
6FFH Crystal Structure of mGluR5 in complex with Fenobam at 2.65 A Deposited 2018-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 569–678（110 aa） Fragment：MGLUR5
Chain A 679–836（158 aa） Fragment：MGLUR5
Mutation：C54T C97A E579A N667Y I669A G675M T742A S753A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C54T C97A E579A N667Y I669A G675M T742A S753A Non-standard monomer：Yes (specific site not provided by mmCIF) OLA OLEIC ACID × 5 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 D7W 1-(3-chlorophenyl)-3-(3-methyl-5-oxidanylidene-4~{H}-imidazol-2-yl)urea × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.8；293.1 K；24-34% V/V PEG400, 0.2 M AMMONIUM PHOSPHATE DIBASIC, 0.1 M MES, PH 6.8
Resolution 2.65 Å R-free 0.267
6FFI Crystal Structure of mGluR5 in complex with MMPEP at 2.2 A Deposited 2018-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 569–678（110 aa） Fragment：MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5
Chain A 680–836（157 aa） Fragment：MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5
Mutation：;E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A ; Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：;E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A ; Non-standard monomer：Yes (specific site not provided by mmCIF) OLA OLEIC ACID × 7 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 D8B 2-[2-(3-methoxyphenyl)ethynyl]-6-methyl-pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.8；293.1 K；24-34% V/V PEG400, 0.2 M AMMONIUM PHOSPHATE DIBASIC, 0.1 M MES, PH 6.8
Resolution 2.20 Å R-free 0.269
6N4X Metabotropic Glutamate Receptor 5 Apo Form Ligand Binding Domain Deposited 2018-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 20–865（846 aa）
Chain B 20–865（846 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；15% PEG 3350, 0.2M Na Cacodylate pH 6.5
Resolution 4.00 Å R-free 0.282
6N4Y Metabotropic Glutamate Receptor 5 Extracellular Domain with Nb43 Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–571（551 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18-20% PEG 3350 0.15M Potassium Nitrate 1% Benzamidine
Resolution 3.26 Å R-free 0.251
6N4Y Metabotropic Glutamate Receptor 5 Extracellular Domain with Nb43 Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–571（551 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18-20% PEG 3350 0.15M Potassium Nitrate 1% Benzamidine
Resolution 3.26 Å R-free 0.251
6N4Y Metabotropic Glutamate Receptor 5 Extracellular Domain with Nb43 Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 21–571（551 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18-20% PEG 3350 0.15M Potassium Nitrate 1% Benzamidine
Resolution 3.26 Å R-free 0.251
6N4Y Metabotropic Glutamate Receptor 5 Extracellular Domain with Nb43 Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 21–571（551 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18-20% PEG 3350 0.15M Potassium Nitrate 1% Benzamidine
Resolution 3.26 Å R-free 0.251
6N50 Metabotropic Glutamate Receptor 5 Extracellular Domain in Complex with Nb43 and L-quisqualic acid Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–571（551 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM NaCl 50 mM ADA pH 7.0 20% PEG 4000
Resolution 3.75 Å R-free 0.300
6N50 Metabotropic Glutamate Receptor 5 Extracellular Domain in Complex with Nb43 and L-quisqualic acid Deposited 2018-11-20 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 21–571（551 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM NaCl 50 mM ADA pH 7.0 20% PEG 4000
Resolution 3.75 Å R-free 0.300
6N50 Metabotropic Glutamate Receptor 5 Extracellular Domain in Complex with Nb43 and L-quisqualic acid Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 21–571（551 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM NaCl 50 mM ADA pH 7.0 20% PEG 4000
Resolution 3.75 Å R-free 0.300
6N51 Metabotropic Glutamate Receptor 5 bound to L-quisqualate and Nb43 Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 23–826（804 aa）
Chain B 23–826（804 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；additional 0.1%OG was added to the sample right before applying sample to grid; 3.5ul sample was applied; blot for 1 second before plunging;
Resolution 4.00 Å
6N52 Metabotropic Glutamate Receptor 5 Apo Form Deposited 2018-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 20–839（820 aa）
Chain B 20–839（820 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；100mM NaCl, 20 mM HEPES pH 7.5, 5uM FFMTEB added as a negative allosteric modulator.
cryo-EM vitrification conditions Cryogen ETHANE；Addition 0.0005% Amphipol A8-35was added to sample prior to apply to grid; 3.5ul sample was applied; blot for 1s before plunging
Resolution 4.00 Å
7FD8 Thermostabilised full length human mGluR5-5M bound with L-quisqualic acid Deposited 2021-07-16 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–856（836 aa）
Chain B 21–856（836 aa）
Mutation：H350L, N445A, T742A, S753A, T777A, I799A, A813L Mutation：H350L, N445A, T742A, S753A, T777A, I799A, A813L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 Y01 CHOLESTEROL HEMISUCCINATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blot force was 10, 3.5 seconds blotting time
Resolution 3.80 Å
7FD9 Thermostabilised full length human mGluR5-5M with orthosteric antagonist, LY341495 Deposited 2021-07-16 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–856（836 aa）
Chain B 21–856（836 aa）
Mutation：H350L, N445A, T742A, S753A, T777A, I799A, A813L Mutation：H350L, N445A, T742A, S753A, T777A, I799A, A813L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 Z99 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blot force was 10, 3.5 seconds blotting time
Resolution 4.00 Å
7P2L thermostabilised 7TM domain of human mGlu5 receptor bound to photoswitchable ligand alloswitch-1 Deposited 2021-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 569–678（110 aa）
Chain A 679–836（158 aa）
Mutation：E579A,N667Y,I669A,G675M,T742A,S753A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E579A,N667Y,I669A,G675M,T742A,S753A Non-standard monomer：Yes (specific site not provided by mmCIF) 4YI 2-chloranyl-~{N}-[2-methoxy-4-[(~{E})-pyridin-2-yldiazenyl]phenyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；295 K；0.15-0.25 M ammonium phosphate dibasic, 22-24 % polyethylene glycol 400, either with 0.10 M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.7-6.8 or 0.1 M HEPES pH 6.8
Resolution 2.54 Å R-free 0.285
8T6J CDPPB-bound inactive mGlu5 Deposited 2023-06-16 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 20–876（857 aa）
Chain B 20–876（857 aa）
Not recorded YKU 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8T7H Quis-bound intermediate mGlu5 Deposited 2023-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 20–876（857 aa）
Chain B 20–876（857 aa）
Not recorded QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8T8M Quis-bound intermediate mGlu5 Deposited 2023-06-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 20–876（857 aa）
Chain B 20–876（857 aa）
Not recorded QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8TAO Quis and CDPPB bound active mGlu5 Deposited 2023-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 20–876（857 aa）
Chain B 20–876（857 aa）
Not recorded QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 YKU 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8X0B Human FL Metabotropic glutamate receptor 5, mGlu5-5M with Quisqualate and VU0424465 Deposited 2023-11-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–856（836 aa）
Chain B 21–856（836 aa）
Mutation：T742A, S753A, T777A, I799A, A813L,N445,H350L Mutation：T742A, S753A, T777A, I799A, A813L,N445,H350L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 XQT VU0424465 × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8X0C Human FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqualate and VU0424465, conformer 1 Deposited 2023-11-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–856（836 aa）
Chain B 21–856（836 aa）
Mutation：T742A,S753A,T777A,I799A,A813L,N455A,H350L Mutation：T742A,S753A,T777A,I799A,A813L,N455A,H350L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 XQT VU0424465 × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blotting time was 5 seconds, blot force of 10
Resolution 3.20 Å
8X0D Human FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqualate and VU0424465, conformer 2 Deposited 2023-11-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–856（836 aa）
Chain B 21–856（836 aa）
Mutation：T742A,S753A,T777A,I799A,A813L,N445A,H350L Mutation：T742A,S753A,T777A,I799A,A813L,N445A,H350L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 XQT VU0424465 × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blotting time of 5 seconds and blot force of 10
Resolution 3.50 Å
8X0E Human FL Metabotropic glutamate receptor 5, mGlu5-5M with agonist and PAM, W785A mutant Deposited 2023-11-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–856（836 aa）
Chain B 21–856（836 aa）
Mutation：T742A,S753A,T777A,I799A,A813L,W785A,H350L Mutation：T742A,S753A,T777A,I799A,A813L,W785A,H350L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blot force was set to 0
Resolution 3.40 Å
8X0F Human FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqualate and PAM VU29 Deposited 2023-11-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–856（836 aa）
Chain B 21–856（836 aa）
Mutation：T742A, S753A, T777A, I799A, A813L,N445A,H350L Mutation：T742A, S753A, T777A, I799A, A813L,N445A,H350L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 XRQ N-(1,3-diphenyl-1H-pyrazol-5-yl)-4-nitrobenzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8X0G Human FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqualate, Acc conformation (purified with PAM VU0409551 but not modelled) Deposited 2023-11-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–856（836 aa）
Chain B 21–856（836 aa）
Mutation：T742A, S753A, T777A, I799A, A813L,N445A,H350L Mutation：T742A, S753A, T777A, I799A, A813L,N445A,H350L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8X0H Human FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqualate, Rcc conformation Deposited 2023-11-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–856（836 aa）
Chain B 21–856（836 aa）
Mutation：T742A, S753A, T777A, I799A, A813L,N445A,H350L Mutation：T742A, S753A, T777A, I799A, A813L,N445A,H350L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9HC0 Dark structure of the human metabotropic glutamate receptor 5 transmembrane domain bound to photoswitchable ligand alloswitch-1 Deposited 2024-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 569–678（110 aa）
Chain A 680–836（157 aa）
Mutation：E579A,N667Y,I669A,G675M,T742A,S753A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E579A,N667Y,I669A,G675M,T742A,S753A Non-standard monomer：Yes (specific site not provided by mmCIF) OLA OLEIC ACID × 5 4YI 2-chloranyl-~{N}-[2-methoxy-4-[(~{E})-pyridin-2-yldiazenyl]phenyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.2；293 K；PEG300, di-ammonium hydrogen phosphate, 1,6-hexanediol, BIS-TRIS
Resolution 2.33 Å R-free 0.271
9HC3 Apo-state structure of the human metabotropic glutamate receptor 5 transmembrane domain freeze-trapped after light activation of photoswitchable ligand alloswitch-1 Deposited 2024-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 569–678（110 aa）
Chain A 680–836（157 aa）
Mutation：E579A,N667Y,I669A,G675M,T742A,S753A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E579A,N667Y,I669A,G675M,T742A,S753A Non-standard monomer：Yes (specific site not provided by mmCIF) OLA OLEIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.2；293 K；PEG300, di-ammonium hydrogen phosphate, 1,6-hexanediol, BIS-TRIS
Resolution 2.90 Å R-free 0.302
9WQK GRM5-Gi Complex Structure Deposited 2025-09-11 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 X 21–839（819 aa）
Chain Y 21–839（819 aa）
Not recorded YKU 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide × 1 GGL GAMMA-L-GLUTAMIC ACID × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CL CHLORIDE ION × 2 CLR CHOLESTEROL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9WQL GRM5-Gq Complex Structure Deposited 2025-09-11 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 X 21–839（819 aa）
Chain Y 21–839（819 aa）
Not recorded YKU 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide × 1 GGL GAMMA-L-GLUTAMIC ACID × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CL CHLORIDE ION × 2 CLR CHOLESTEROL × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

28 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GRM5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–492； UniProt 18–505 Author chain B； PDBConstruct 5–492； UniProt 18–505

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

SAXS scattering curve SAXS Profile

SAXS profile for 3lmk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3lmk
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3lmk
Deposition date deposition_date2010-01-30
Structure title titleLigand Binding Domain of Metabotropoc glutamate receptor mGluR5 complexed with glutamate
Keywords keywords;GLUTAMATE RECEPTORS, MGLUR1, DIMERIZATION, GLUTAMIC ACID, Cell membrane, G-protein coupled receptor, Glycoprotein, Membrane, Receptor, Transducer, Transmembrane, Structural Genomics, Structural Genomics Consortium, SGC, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier30.12 Å
Radius of gyration Rg (electron density) rg_electron29.15 Å
Forward intensity I(0) i0153033000.00
Molecular weight molecular_weight96809.0 kDa
Excluded volume excluded_volume120510 ų
Envelope volume envelope_volume149050 ų
Hydration-shell volume shell_volume41370 ų
Envelope diameter envelope_diameter99.8 Å
Shell Rg shell_rg37.45 Å
Envelope Rg envelope_rg29.31 Å
Shape Rg shape_rg29.16 Å
Total Rg total_rg29.89 Å
Total atoms total_atoms6795
Residues n_residues877
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax94.8 Å
Rg (real space) rg_real30.01 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real1.5300e+08
I(0) uncertainty (real space) i0_real_error2.1430e+06
Rg (reciprocal space) rg_reciprocal30.06 Å
I(0) (reciprocal space) i0_reciprocal153000000.0000
Solution quality estimate total_estimate0.6826
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.8 Å
Skewness Skewness skewness0.211
Kurtosis Kurtosis kurtosis-0.503
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43310000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 0.050; Positv: 1.000; Valcen: 0.997; Smooth: 0.936
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3lmka_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd3lmkb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (4 domains)

Domain ID domain_id3lmkA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3lmkA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3lmkB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3lmkB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
▶

8. Citations (1)

▶

9. Files and Curves (10)