SAXSdb — 9bvh

▼

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

Glycine receptor subunit alpha-3

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	Other combination Homooligomer Protein × 5 其他Polymer 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–464 Chain B； UniProt 1–464 Chain C； UniProt 1–464 Chain D； UniProt 1–464 Chain E； UniProt 1–464	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 20 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 CLR CHOLESTEROL × 5	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.58 Å

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 9BVH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CFB Crystal Structure of Human Glycine Receptor alpha-3 Bound to Strychnine Deposited 2015-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain A 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain B 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain B 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain C 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain C 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain D 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain D 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain E 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain E 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted	Not recorded	SY9 STRYCHNINE × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；30-33% PEG-400, 200 mM magnesium chloride, 100 mM potassium chloride, 25 mM sodium citrate	Resolution 3.04 Å R-free 0.283
5TIN Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607 Deposited 2016-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain A 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain B 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain B 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain C 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain C 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain D 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain D 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain E 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain E 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted	Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q	7C6 (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one × 5 GLY GLYCINE × 5 ZN ZINC ION × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM Calcium Chloride, 22.5-27.5% PEG-350MME, 100 mM MES	Resolution 2.61 Å R-free 0.214
5TIO Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607 Deposited 2016-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain A 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain B 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain B 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain C 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain C 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain D 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain D 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain E 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted Chain E 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted	Not recorded	7C6 (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one × 5 GLY GLYCINE × 5 ZN ZINC ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM Calcium Chloride, 22.5-27.5% PEG-350MME, 100 mM MES	Resolution 3.25 Å R-free 0.254
5VDH Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607, Glycine, and Ivermectin Deposited 2017-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain A 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain B 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain B 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain C 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain C 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain D 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain D 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain E 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain E 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460	Not recorded	7C6 (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one × 5 GLY GLYCINE × 5 IVM (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside × 5 ZN ZINC ION × 5 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM calcium chloride, 22.5-27.5% PEG350 MME, 100 mM MES, pH 6.5	Resolution 2.85 Å R-free 0.236
5VDI Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607, Glycine, and Ivermectin Deposited 2017-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain A 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain B 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain B 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain C 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain C 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain D 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain D 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain E 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460 Chain E 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460	Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q	7C6 (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one × 5 GLY GLYCINE × 5 IVM (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside × 5 ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM calcium chloride, 22.5-27.5% PEG350 MME, 100 mM MES, pH 6.5	Resolution 3.10 Å R-free 0.256
9BOY Cryo-EM structure of human Glycine Receptor apha3-beta heteromer with glycine in nanodisc Deposited 2024-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 34–464（431 aa） Chain B 34–464（431 aa） Chain C 34–464（431 aa） Chain D 34–464（431 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLY GLYCINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.81 Å
9BOZ Cryo-EM structure of human Glycine Receptor alpha3-beta heteromer in presence of glycine Deposited 2024-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 34–464（431 aa） Chain B 34–464（431 aa） Chain C 34–464（431 aa） Chain D 34–464（431 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
9BP0 Cryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta with glycine Deposited 2024-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 34–464（431 aa） Chain B 34–464（431 aa） Chain C 34–464（431 aa） Chain D 34–464（431 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLY GLYCINE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å
9BP7 Cryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta in presence of glycine and 2,6-DTBP Deposited 2024-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 34–464（431 aa） Chain B 34–464（431 aa） Chain C 34–464（431 aa） Chain D 34–464（431 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLY GLYCINE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BU2 Homomeric alpha3 glycine receptor in the presence of 1 mM glycine at pH 6.4 in a desensitized state Deposited 2024-05-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–464（464 aa） Chain B 1–464（464 aa） Chain C 1–464（464 aa） Chain D 1–464（464 aa） Chain E 1–464（464 aa）	Not recorded	GLY GLYCINE × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 6.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
9BU3 Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine in a desensitized state Deposited 2024-05-16	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–464（464 aa） Chain B 1–464（464 aa） Chain C 1–464（464 aa） Chain D 1–464（464 aa） Chain E 1–464（464 aa）	Not recorded	GLY GLYCINE × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9BVJ Homomeric alpha3 glycine receptor in the presence of 1 mM glycine in an desensitized state. Deposited 2024-05-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–464（464 aa） Chain B 1–464（464 aa） Chain C 1–464（464 aa） Chain D 1–464（464 aa） Chain E 1–464（464 aa）	Not recorded	GLY GLYCINE × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9BWB Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in a desensitized state Deposited 2024-05-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–464（464 aa） Chain B 1–464（464 aa） Chain C 1–464（464 aa） Chain D 1–464（464 aa） Chain E 1–464（464 aa）	Not recorded	GLY GLYCINE × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 6.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.21 Å
9BWC Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in an apo state Deposited 2024-05-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–464（464 aa） Chain B 1–464（464 aa） Chain C 1–464（464 aa） Chain D 1–464（464 aa） Chain E 1–464（464 aa）	Not recorded	PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 25 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 5 GLY GLYCINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 6.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.19 Å
9BWE Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in an intermediate state Deposited 2024-05-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–464（464 aa） Chain B 1–464（464 aa） Chain C 1–464（464 aa） Chain D 1–464（464 aa） Chain E 1–464（464 aa）	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 30 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 GLY GLYCINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 6.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
9BWG Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine and 0.1 mM zinc in a desensitized state Deposited 2024-05-21	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–464（464 aa） Chain B 1–464（464 aa） Chain C 1–464（464 aa） Chain D 1–464（464 aa） Chain E 1–464（464 aa）	Not recorded	GLY GLYCINE × 5 ZN ZINC ION × 10 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.59 Å
9BWJ Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine and 0.1 mM zinc in an apo state Deposited 2024-05-21	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–464（464 aa） Chain B 1–464（464 aa） Chain C 1–464（464 aa） Chain D 1–464（464 aa） Chain E 1–464（464 aa）	Not recorded	ZN ZINC ION × 10 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 35	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.21 Å
9BZP Homomeric alpha3 glycine receptor in the presence of 0.1 millimolar glycine and 1 micromolar zinc in a desensitized state Deposited 2024-05-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–464（464 aa） Chain B 1–464（464 aa） Chain C 1–464（464 aa） Chain D 1–464（464 aa） Chain E 1–464（464 aa）	Not recorded	GLY GLYCINE × 5 ZN ZINC ION × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GLRA3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–464； UniProt 1–464 Author chain B； PDBConstruct 1–464； UniProt 1–464 Author chain C； PDBConstruct 1–464； UniProt 1–464 Author chain D； PDBConstruct 1–464； UniProt 1–464 Author chain E； PDBConstruct 1–464； UniProt 1–464

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9bvh
Deposition date deposition_date	2024-05-20
Structure title title	Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine in an apo state.
Keywords keywords	Glycine, Ion Channel, Ligand-Gated, Pentameric, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	40.19 Å
Radius of gyration Rg (electron density) rg_electron	39.85 Å
Forward intensity I(0) i0	541213000.00
Molecular weight molecular_weight	208170.0 kDa
Excluded volume excluded_volume	267790 Å³
Envelope volume envelope_volume	353180 Å³
Hydration-shell volume shell_volume	72075 Å³
Envelope diameter envelope_diameter	133.6 Å
Shell Rg shell_rg	46.82 Å
Envelope Rg envelope_rg	39.49 Å
Shape Rg shape_rg	39.86 Å
Total Rg total_rg	40.21 Å
Total atoms total_atoms	14660
Residues n_residues	1710
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	132.8 Å
Rg (real space) rg_real	40.15 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	5.4120e+08
I(0) uncertainty (real space) i0_real_error	9.4840e+06
Rg (reciprocal space) rg_reciprocal	40.19 Å
I(0) (reciprocal space) i0_reciprocal	541200000.0000
Solution quality estimate total_estimate	0.8760
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.7 Å
Skewness Skewness skewness	0.353
Kurtosis Kurtosis kurtosis	-0.305
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	106100000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.902

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Glycine receptor subunit alpha-3
Molecular weight formula_weight	55581.1 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	14680

MAHVRHFRTLVSGFYFWEAALLLSLVATKETDSARSRSAPMSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQKWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRIFKNGNVLYSIRLTLTLSCPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWQDEAPVQVAEGLTLPQFLLKEEKDLRYCTKHYNTGKFTCIEVRFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFVSRQHKELLRFRRKRKNKTEAFALEKFYRFSDMDDEVRESRFSFTAYGMGPCLQAKDGMTPKGPNHPVQVMPKSPDEMRKVFIDRAKKIDTISRACFPLAFLIFNIFYWVIYKILRHEDIHQQQDLVPRGSHHHHHHHH

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 aff. frugiperda 1 BOLD-2017

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	;[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate ;
Molecular weight formula_weight	746.6 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 4 Entity 4 non-polymer

Description description	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	678.9 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 5 Entity 5 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.58 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	106791

fit	/app/data/saxs_computation/bv/9bvh/9bvh.fit
pddf	/app/data/pr_computation/bv/9bvh/9bvh.pr.out
profile	/app/data/saxs_computation/bv/9bvh/9bvh.dat

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine in an apo state.

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

Glycine receptor subunit alpha-3

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