2bfw

Structure of the C domain of glycogen synthase from Pyrococcus abyssi

Method: X-RAY DIFFRACTION D_max: 51.5 Å Quality: GOOD

▼

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

GLGA GLYCOGEN SYNTHASE

PYROCOCCUS ABYSSI

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 218–413	Fragment：CATALYTIC DOMAIN, RESIDUES 218-413	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

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 2BFW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BIS Structure of glycogen synthase from Pyrococcus abyssi Deposited 2005-01-25	Different construct 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 construct 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 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
6ME5 XFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine Deposited 2018-09-05	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 218–413（196 aa）	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
6PS8 XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin. Deposited 2019-07-12	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 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 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 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 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 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 construct Different mutation/modification Different oligomeric state 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 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 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 construct 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 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 construct 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）	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 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 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 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 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 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 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 construct Different oligomeric state 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 construct Different oligomeric state 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 construct 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 construct 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 construct 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 construct 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
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–200； 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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2bfw
Deposition date deposition_date	2004-12-15
Structure title title	Structure of the C domain of glycogen synthase from Pyrococcus abyssi
Keywords keywords	GLYCOSYLTRANSFERASE FAMILY 5 UDP/ADP-GLUCOSE-GLYCOGEN SYNTHASE TWO ROSSMAN FOLDS, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.17 Å
Radius of gyration Rg (electron density) rg_electron	15.62 Å
Forward intensity I(0) i0	9161500.00
Molecular weight molecular_weight	22311.0 kDa
Excluded volume excluded_volume	27931 Å³
Envelope volume envelope_volume	31088 Å³
Hydration-shell volume shell_volume	16299 Å³
Envelope diameter envelope_diameter	51.2 Å
Shell Rg shell_rg	22.04 Å
Envelope Rg envelope_rg	15.87 Å
Shape Rg shape_rg	15.60 Å
Total Rg total_rg	16.75 Å
Total atoms total_atoms	1560
Residues n_residues	196
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

▼

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

Maximum dimension Dmax dmax	51.5 Å
Rg (real space) rg_real	17.01 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	9.1620e+06
I(0) uncertainty (real space) i0_real_error	1.0680e+05
Rg (reciprocal space) rg_reciprocal	17.03 Å
I(0) (reciprocal space) i0_reciprocal	9162000.0000
Solution quality estimate total_estimate	0.8993
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	-0.010
Kurtosis Kurtosis kurtosis	-0.513
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2480000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.991

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	GLGA GLYCOGEN SYNTHASE
Molecular weight formula_weight	22251.7 kDa
EC 编号 ec_number	2.4.1.21
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	1866

GSHNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFS

来源 Source

来源生物 organism	PYROCOCCUS ABYSSI
NCBI Class编号 ncbi_taxonomy_id	29292
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2bfwa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
Family Family family	c.87.1.8 — Glycosyl transferases group 1

CATH v4.4 (1 domains)

Domain ID domain_id	2bfwA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

▶

8. Citations (1)

▶

Unit-cell length a length_a	39.614 Å
Unit-cell length b length_b	50.820 Å
Unit-cell length c length_c	44.261 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	42.330 Å
R factor r_factor	0.1860
R_work r_work	0.1830
R_free r_free	0.2350

fit	/app/data/saxs_computation/bf/2bfw/2bfw.fit
pddf	/app/data/pr_computation/bf/2bfw/2bfw.pr.out
profile	/app/data/saxs_computation/bf/2bfw/2bfw.dat