6me5

XFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine

Method: X-RAY DIFFRACTION D_max: 100.1 Å Quality: REASONABLE

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

chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 12–218 Chain A； UniProt 228–325	Non-standard monomer：Yes (specific site not provided by mmCIF)	AWY ~{N}-[2-(7-methoxynaphthalen-1-yl)ethyl]ethanamide × 1 OLA OLEIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol	Resolution 3.20 Å R-free 0.257

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 6ME5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6ME2 XFEL crystal structure of human melatonin receptor MT1 in complex with ramelteon Deposited 2018-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 12–218（207 aa） Chain A 228–325（98 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	JEV N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide × 1 OLA OLEIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol	Resolution 2.80 Å R-free 0.228
6ME3 XFEL crystal structure of human melatonin receptor MT1 in complex with 2-phenylmelatonin Deposited 2018-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 12–218（207 aa） Chain A 228–325（98 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 OLA OLEIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol	Resolution 2.90 Å R-free 0.229
6ME4 XFEL crystal structure of human melatonin receptor MT1 in complex with 2-iodomelatonin Deposited 2018-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 12–218（207 aa） Chain A 228–325（98 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ML2 N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol	Resolution 3.20 Å R-free 0.249
6PS8 XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin. Deposited 2019-07-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 12–218（207 aa） Chain A 228–325（98 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 100 mM HEPES pH 7.0, 32-35% PEG 400, 1 mM of target ligand 2-phenylmelatonin, 2.5% DMSO, 1.5% propan-2-ol.	Resolution 3.30 Å R-free 0.307
7DB6 human melatonin receptor MT1 - Gi1 complex Deposited 2020-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–340（340 aa）	Not recorded	JEV N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7VGY Melatonin receptor1-2-Iodomelatonin-Gicomplex Deposited 2021-09-20	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 × 5 PDB declaration: pentameric	Chain A 1–350（350 aa）	Not recorded	CLR CHOLESTEROL × 1 ML2 N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7VGZ MT1-remalteon-Gi complex Deposited 2021-09-20	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 × 5 PDB declaration: pentameric	Chain B 1–350（350 aa）	Not recorded	JEV N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MTR1A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–209； UniProt 12–218 Author chain A； PDBConstruct 406–503； UniProt 228–325

chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase

Homo sapiens

UniProt Q9V2J8

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 218–413	Non-standard monomer：Yes (specific site not provided by mmCIF)	AWY ~{N}-[2-(7-methoxynaphthalen-1-yl)ethyl]ethanamide × 1 OLA OLEIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol	Resolution 3.20 Å R-free 0.257

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6ME5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BFW Structure of the C domain of glycogen synthase from Pyrococcus abyssi Deposited 2004-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 218-413	Not recorded	SO4 SULFATE ION × 4 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；30% PEG8K, 0.1 M NAAC PH 4.5, 0.2M LITHIUM SULPHATE	Resolution 1.80 Å R-free 0.235
2BIS Structure of glycogen synthase from Pyrococcus abyssi Deposited 2005-01-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–437（437 aa）	Not recorded	GLC alpha-D-glucopyranose × 1 DIO 1,4-DIETHYLENE DIOXIDE × 4 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.60	Resolution 2.80 Å R-free 0.266
2BIS Structure of glycogen synthase from Pyrococcus abyssi Deposited 2005-01-25	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 1–437（437 aa）	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 3 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.60	Resolution 2.80 Å R-free 0.266
2BIS Structure of glycogen synthase from Pyrococcus abyssi Deposited 2005-01-25	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 1–437（437 aa）	Not recorded	GLC alpha-D-glucopyranose × 1 DIO 1,4-DIETHYLENE DIOXIDE × 3 GOL GLYCEROL × 1 UDP URIDINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.60	Resolution 2.80 Å R-free 0.266
3FRO Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations Deposited 2009-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–437（437 aa） Chain B 1–437（437 aa） Chain C 1–437（437 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 PO4 PHOSPHATE ION × 3 NHF 1,5-anhydro-D-fructose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；26-30% MPD, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.255
3L01 Crystal structure of monomeric glycogen synthase from Pyrococcus abyssi Deposited 2009-12-09	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 1–426（426 aa） Fragment：UNP residues 1-426	Mutation：T426A	K POTASSIUM ION × 3 CL CHLORIDE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；ammonium sulfate, potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.228
3L01 Crystal structure of monomeric glycogen synthase from Pyrococcus abyssi Deposited 2009-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–426（426 aa） Fragment：UNP residues 1-426	Mutation：T426A	K POTASSIUM ION × 3 CL CHLORIDE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；ammonium sulfate, potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.228
4S0V Crystal structure of the human OX2 orexin receptor bound to the insomnia drug Suvorexant Deposited 2015-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa） Fragment：UNP O43614 residues 3-254, 294-388, and UNP Q9V2J8 residues 218-413	Not recorded	SUV [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 OLA OLEIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions Lipidic Cubic Phase (LCP)；pH 5.9；293 K；31% PEG 400, 0.1 M sodium citrate, 0.2 M sodium formate, 3%(w/v) hexanediol, pH 5.9, Lipidic Cubic Phase (LCP), temperature 293K	Resolution 2.50 Å R-free 0.242
4ZJ8 Structures of the human OX1 orexin receptor bound to selective and dual antagonists Deposited 2015-04-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa） Fragment：UNP O43613 residues 1-245,UNP Q9V2J8 residues 218-413,UNP O43613 residues 288-380	Not recorded	SUV [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 OLA OLEIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.4；293 K；100mM Sodium Citrate pH 5.4, 31% PEG 400, 200 mM Sodium Formate	Resolution 2.75 Å R-free 0.273
4ZJC Structures of the human OX1 orexin receptor bound to selective and dual antagonists Deposited 2015-04-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa） Fragment：UNP O43613 residues 1-245,UNP Q9V2J8 residues 218-413,UNP O43613 residues 288-380	Not recorded	4OT [5-(2-fluorophenyl)-2-methyl-1,3-thiazol-4-yl]{(2S)-2-[(5-phenyl-1,3,4-oxadiazol-2-yl)methyl]pyrrolidin-1-yl}methanone × 1 OLA OLEIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.6；293 K；100 mM Sodium Citrate pH 5.6, 32% PEG 400, 200 mM Potossium	Resolution 2.83 Å R-free 0.262
5U09 High-resolution crystal structure of the human CB1 cannabinoid receptor Deposited 2016-11-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa） Fragment：P21554 residues 90-301, 333-421 and Q9V2J8 residues 218-413	Mutation：T210A	PEG DI(HYDROXYETHYL)ETHER × 9 SO4 SULFATE ION × 4 7DY N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；31% PEG400, 100mM Sodium Citrate pH5.5, 100mM magnesium sulfate	Resolution 2.60 Å R-free 0.238
5WQC Crystal structure of human orexin 2 receptor bound to the selective antagonist EMPA determined by the synchrotron light source at SPring-8. Deposited 2016-11-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa） Fragment：UNP residues 3-254,UNP residues 218-413,UNP residues 294-386	Not recorded	7MA N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide × 1 OLA OLEIC ACID × 5 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；50 mM MES-NaOH (pH 5.8-6.2), 26-29% PEG300, 100 mM sodium malonate, 0.5 mM EMPA, 5% DMSO	Resolution 1.96 Å R-free 0.215
5WS3 Crystal structures of human orexin 2 receptor bound to the selective antagonist EMPA determined by serial femtosecond crystallography at SACLA Deposited 2016-12-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa） Fragment：UNP residues 3-254,UNP residues 218-413,UNP residues 294-388	Not recorded	7MA N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide × 1 OLA OLEIC ACID × 4 1PE PENTAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；0.1M MES, 0.1M sodium malonate, 27-30% PEG 300, pH 6.0	Resolution 2.30 Å R-free 0.219
6E59 Crystal structure of the human NK1 tachykinin receptor Deposited 2018-07-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa） Fragment：receptor (UNP residues 1-227, 238-346) with intervening glycogen synthase (UNP residues 218-413)	Not recorded	L76 1-(4-{[(2R,3S)-2-{(1R)-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy}-3-(4-fluorophenyl)morpholin-4-yl]methyl}-1H-1,2,3-triazol-5-yl)-N,N-dimethylmethanamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM sodium citrate, pH 5.4, 30% PEG300, 200 mM potassium nitrate, 2% 2,5-hexanediol	Resolution 3.40 Å R-free 0.305
6FJ3 High resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist. Deposited 2018-01-19	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 218–413（196 aa）	Mutation：;Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A ; Non-standard monomer：Yes (specific site not provided by mmCIF)	MAN alpha-D-mannopyranose × 3 OLA OLEIC ACID × 9 ACY ACETIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；0.1 M sodium citrate pH 6.0, 0.3 M sodium acetate, 31% PEG400, 20 uM E-PTH(1-34)	Resolution 2.50 Å R-free 0.248
6HLL Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist CP-99,994 Deposited 2018-09-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 220–413（194 aa）	Mutation：;L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A ;	GBK (2~{S},3~{S})-~{N}-[(2-methoxyphenyl)methyl]-2-phenyl-piperidin-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM MES pH 6.0, 31% (v/v) PEG400, 190-210 mM potassium acetate, 2.4% (v/v) 2,5-hexanediol and 50 uM CP-99,994	Resolution 3.27 Å R-free 0.275
6HLO Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist Aprepitant Deposited 2018-09-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 220–413（194 aa）	Mutation：;L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A ; Non-standard monomer：Yes (specific site not provided by mmCIF)	GBQ 5-[[(2~{R},3~{S})-2-[(1~{R})-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy]-3-(4-fluorophenyl)morpholin-4-yl]methyl]-1,2-dihydro-1,2,4-triazol-3-one × 1 CIT CITRIC ACID × 1 OLA OLEIC ACID × 17 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 3	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM sodium citrate pH 6.0, 31% (v/v) PEG400, 50-70 mM MgCl2 and 50 uM aprepitant	Resolution 2.40 Å R-free 0.229
6HLP Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist Netupitant Deposited 2018-09-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 220–413（194 aa）	Mutation：;L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A ; Non-standard monomer：Yes (specific site not provided by mmCIF)	GAW 2-[3,5-bis(trifluoromethyl)phenyl]-~{N},2-dimethyl-~{N}-[4-(2-methylphenyl)-6-(4-methylpiperazin-1-yl)pyridin-3-yl]propanamide × 1 CIT CITRIC ACID × 1 OLA OLEIC ACID × 9 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 7 PEG DI(HYDROXYETHYL)ETHER × 24	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM sodium citrate pH 6.0, 31% (v/v) PEG400, 40-50 mM Mg(HCO2)2 and 50 uM netupitant	Resolution 2.20 Å R-free 0.225
6KP6 The structural study of mutation induced inactivation of Human muscarinic receptor M4 Deposited 2019-08-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Mutation：I93T G150A I187A S219Y N449R T459E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.8；293.15 K；300 mM diammonium hydrogen phosphate, 22-26% PEG 300, 0.1M HEPES sodium pH 7.6-8.2	Resolution 3.00 Å R-free 0.264
6KQI Structure of an allosteric modulator bound to the CB1 cannabinoid receptor Deposited 2019-08-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa） Fragment：C1	Mutation：S203K,T210A,E273K,T283V,R340E	9GF 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol × 1 9GL 5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide × 1 OLA OLEIC ACID × 4 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；33% PEG 400, 100mM Sodium Cacodylate pH 6.0, 100mM Sodium Malonate	Resolution 3.25 Å R-free 0.312
6LFL Crystal structure of a class A GPCR Deposited 2019-12-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Mutation：L135W, A249E, G303A	EBX 4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl)propyl]amino]cyclobuten-1-yl]amino]-~{N},~{N}-dimethyl-3-oxidanyl-pyridine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM HEPES pH7.0, 32% PEG 400, 50-150 mM Sodium tartrate dibasic dihydrate salt	Resolution 3.20 Å R-free 0.264
6ME2 XFEL crystal structure of human melatonin receptor MT1 in complex with ramelteon Deposited 2018-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	JEV N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide × 1 OLA OLEIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol	Resolution 2.80 Å R-free 0.228
6ME3 XFEL crystal structure of human melatonin receptor MT1 in complex with 2-phenylmelatonin Deposited 2018-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 OLA OLEIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol	Resolution 2.90 Å R-free 0.229
6ME4 XFEL crystal structure of human melatonin receptor MT1 in complex with 2-iodomelatonin Deposited 2018-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ML2 N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol	Resolution 3.20 Å R-free 0.249
6PS8 XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin. Deposited 2019-07-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 100 mM HEPES pH 7.0, 32-35% PEG 400, 1 mM of target ligand 2-phenylmelatonin, 2.5% DMSO, 1.5% propan-2-ol.	Resolution 3.30 Å R-free 0.307
6TPG Crystal structure of the Orexin-2 receptor in complex with EMPA at 2.74 A resolution Deposited 2019-12-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Mutation：E54A Y91L D100A V142A R170L L206A Y219A M233A A242L L310V L318A T347A N14D N22D N202D C381W C382W C383W Non-standard monomer：Yes (specific site not provided by mmCIF)	7MA N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide × 1 PG4 TETRAETHYLENE GLYCOL × 1 OLA OLEIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM trisodium citrate buffer 150-300 mM sodium chloride 28-43 % (v/v) polyethylene glycol 400	Resolution 2.74 Å R-free 0.275
6TPJ Crystal structure of the Orexin-2 receptor in complex with suvorexant at 2.76 A resolution Deposited 2019-12-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Mutation：E54A Y91L D100A V142A R170L L206A Y219A M233A A242L L310V L318A T347A N14D N22D N202D C381W C382W C383W Non-standard monomer：Yes (specific site not provided by mmCIF)	OLA OLEIC ACID × 13 SUV [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 NH4 AMMONIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM N-(2-Acetamido)iminodiacetic acid (ADA) 150-300 mM ammonium nitrate 28-43 % (v/v) polyethylene glycol 400	Resolution 2.74 Å R-free 0.254
6TPJ Crystal structure of the Orexin-2 receptor in complex with suvorexant at 2.76 A resolution Deposited 2019-12-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 218–413（196 aa）	Mutation：E54A Y91L D100A V142A R170L L206A Y219A M233A A242L L310V L318A T347A N14D N22D N202D C381W C382W C383W Non-standard monomer：Yes (specific site not provided by mmCIF)	OLA OLEIC ACID × 21 SUV [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 NH4 AMMONIUM ION × 3 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM N-(2-Acetamido)iminodiacetic acid (ADA) 150-300 mM ammonium nitrate 28-43 % (v/v) polyethylene glycol 400	Resolution 2.74 Å R-free 0.254
6TPN Crystal structure of the Orexin-2 receptor in complex with HTL6641 at 2.61 A resolution Deposited 2019-12-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NU8 2-(5,6-dimethoxypyridin-3-yl)-1,1-bis(oxidanylidene)-4-[[2,4,6-tris(fluoranyl)phenyl]methyl]pyrido[2,3-e][1,2,4]thiadiazin-3-one × 1 NO3 NITRATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 OLA OLEIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM trisodium citrate buffer 150-300 mM lithium nitrate or 150-300 mM potassium nitrate 28-43 % (v/v) polyethylene glycol 400	Resolution 2.61 Å R-free 0.251
6V9S Structure-based development of subtype-selective orexin 1 receptor antagonists Deposited 2019-12-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Not recorded	JHC [(2S)-2-[(2S)-butan-2-yl]-4-(5-chloro-1,3-benzoxazol-2-yl)-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 CLR CHOLESTEROL × 1 OLA OLEIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM Sodium Citrate pH 5.3, 31% PEG 400, 200 mM Ammonium Formate	Resolution 3.50 Å R-free 0.273
6W25 Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with SHU9119 Deposited 2020-03-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 218–413（196 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 OLA OLEIC ACID × 8	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.9；293 K；19% PEG 400, 100 mM Bis-tris propane buffer, and 50 mM CaCl2 2H2O	Resolution 2.75 Å R-free 0.259
7BR3 Crystal structure of the protein 1 Deposited 2020-03-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Mutation：P128K	1QW (2R)-2,3-dihydroxypropyl dodecanoate × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 PEG DI(HYDROXYETHYL)ETHER × 6 FMT FORMIC ACID × 1 F5O 4-[[(1R)-2-[5-(2-fluoranyl-3-methoxy-phenyl)-3-[[2-fluoranyl-6-(trifluoromethyl)phenyl]methyl]-4-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]-1-phenyl-ethyl]amino]butanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；100 mM Na cacodyalte pH 6.0-6.5, 30%-38% PEG400, 150-350 mM NH4NO3	Resolution 2.79 Å R-free 0.284
7FEE Crystal structure of the allosteric modulator ZCZ011 binding to CP55940-bound cannabinoid receptor 1 Deposited 2021-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Mutation：S203K,T210A,E273K,T283V,R340E,N393D	CLR CHOLESTEROL × 2 9GF 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol × 1 7IC 6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole × 1 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 4 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 OLA OLEIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；25-36% PEG 300, 100Mm MES pH 6.0, 120-190mM Magnesium Sulfate	Resolution 2.70 Å R-free 0.319
7W41 Crystal Structure of Human Gastrin Releasing Peptide Receptor in complex with the antagonist PD176252 Deposited 2021-11-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Mutation：S127K,I157A,R259E	8B8 (2S)-3-(1H-indol-3-yl)-N-[[1-(5-methoxypyridin-2-yl)cyclohexyl]methyl]-2-methyl-2-[(4-nitrophenyl)carbamoylamino]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.8；294 K；100mM MES, pH 6.8, 300mM Ammonium dihydrogen phosphate, 28% PEG 400, 5% polypropylene glycol P 400	Resolution 2.95 Å R-free 0.321
8CXO Cryo-EM structure of the unliganded mSMO-PGS2 in a lipidic environment Deposited 2022-05-22	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8JHQ Cryo-EM structure of human S1P transporter SPNS2 bound with S1P Deposited 2023-05-25	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–413（196 aa）	Not recorded	S1P (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8KIG Cryo-EM structure of MC3R in complex with SHU9119 Deposited 2023-08-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 218–413（196 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9B9Y Structural mechanism of CB1R binding to peripheral and biased inverse agonists Deposited 2024-04-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 218–413（196 aa）	Not recorded	7DY N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9B9Z Structural mechanism of CB1R binding to peripheral and biased inverse agonists Deposited 2024-04-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 218–413（196 aa）	Not recorded	A1AKO (4S)-3-(4-chlorophenyl)-N'-[(1E)-ethanimidoyl]-4-phenyl-N-[4-(trifluoromethyl)benzene-1-sulfonyl]-4,5-dihydro-1H-pyrazole-1-carboximidamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9BA0 Structural mechanism of CB1R binding to peripheral and biased inverse agonists Deposited 2024-04-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 218–413（196 aa）	Not recorded	A1AKN N-(N-{(E)-[(4S)-3-(4-chlorophenyl)-4-phenyl-4,5-dihydro-1H-pyrazol-1-yl][4-(trifluoromethyl)benzene-1-sulfonamido]methylidene}carbamimidoyl)acetamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9M88 PGS fused GPR3 dimer with antagonist AF64394 Deposited 2025-03-11	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 × 4 PDB declaration: tetrameric	Chain C 218–413（196 aa） Chain D 218–413（196 aa）	Not recorded	5YM (Z)-N-(2-hydroxyethyl)octadec-9-enamide × 2 A1EM1 tetracosan-1-ol × 2 1DO 1-DODECANOL × 8 A1EM3 [(2R)-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-decanoyloxy-propyl] dodecanoate × 4 A1EQ8 icosan-1-ol × 4 A1EM2 N-[(4-chloranyl-2-propan-2-yloxy-phenyl)methyl]-5-phenyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20mM NaCl, 100mM Hepes, 0.003% LMNG, 0.001% GDN cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

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

View Construct and Data Evidence

UniProt name	Q9V2J8_PYRAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 210–405； UniProt 218–413

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	6me5
Deposition date deposition_date	2018-09-05
Structure title title	XFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine
Keywords keywords	GPCR, melatonin receptor type 1A (MT1), agomelatine, membrane protein, XFEL, LCP, PGS, circadian rhythm, jetlag; MEMBRANE 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	30.72 Å
Radius of gyration Rg (electron density) rg_electron	29.87 Å
Forward intensity I(0) i0	38891600.00
Molecular weight molecular_weight	52319.0 kDa
Excluded volume excluded_volume	66871 Å³
Envelope volume envelope_volume	84322 Å³
Hydration-shell volume shell_volume	24840 Å³
Envelope diameter envelope_diameter	103.0 Å
Shell Rg shell_rg	35.15 Å
Envelope Rg envelope_rg	29.87 Å
Shape Rg shape_rg	29.89 Å
Total Rg total_rg	30.38 Å
Total atoms total_atoms	3695
Residues n_residues	484
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	100.1 Å
Rg (real space) rg_real	30.94 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	3.8890e+07
I(0) uncertainty (real space) i0_real_error	6.0660e+05
Rg (reciprocal space) rg_reciprocal	30.85 Å
I(0) (reciprocal space) i0_reciprocal	38890000.0000
Solution quality estimate total_estimate	0.6119
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.362
Kurtosis Kurtosis kurtosis	-0.764
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10320000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 0.077; Positv: 1.000; Valcen: 0.637; Smooth: 0.862

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase
Molecular weight formula_weight	56597.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3695

GTSQPVLRGDGARPSWLASALACVLIFTIVVDILGNLLVILSVYRNKKLRNAGNIFVVSLAVANLVVAIYPYPLVLMSIFNNGWNFGYLHCQVSAFLMGLSVIGSIWNITGIAIDRYLYICHSLKYDKLYSSKNSLCYVLLIWLLTLAAVLPNLRAGTLQYDPRIYSCTFAQSVSSAYTIAVVVFHFLVPMIIVIFCYLRIWILVLQVRGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSKLKPQDFRNFVTMFVVFVLFAICFAPLNFIGLAVASDPASMVPRIPEWLFVASYYMAYFNSCLNPIIYGLLDQNFRKEYRRIIVSLCTARVFFVDSSN

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 2 Entity 2 non-polymer

Description description	~{N}-[2-(7-methoxynaphthalen-1-yl)ethyl]ethanamide
Molecular weight formula_weight	243.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	OLEIC ACID
Molecular weight formula_weight	282.5 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	122.200 Å
Unit-cell length b length_b	122.200 Å
Unit-cell length c length_c	122.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	28.870 Å
R factor r_factor	0.2340
R_work r_work	0.2320
R_free r_free	0.2570

fit	/app/data/saxs_computation/me/6me5/6me5.fit
pddf	/app/data/pr_computation/me/6me5/6me5.pr.out
profile	/app/data/saxs_computation/me/6me5/6me5.dat

XFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine

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

chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase

State in the Current Structure

Other States of the Same Protein in the Database

chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)