SAXSdb — 9pky

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

Glycine receptor, alpha 1

Danio rerio

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Glycine receptor beta subunit 2 × 1 （Q6DC22） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 STRYCHNINE × 5 ;(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	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3DHZ5_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–444； UniProt 1–444 Author chain B； PDBConstruct 1–444； UniProt 1–444 Author chain C； PDBConstruct 1–444； UniProt 1–444 Author chain D； PDBConstruct 1–444； UniProt 1–444

Glycine receptor beta subunit 2

Danio rerio

UniProt Q6DC22

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Glycine receptor, alpha 1 × 4 （B3DHZ5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 STRYCHNINE × 5 ;(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	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6DC22_DANRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–575； UniProt 1–494

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pky
Deposition date deposition_date	2025-07-14
Structure title title	Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 2000 nM ivermectin
Keywords keywords	Ion Channel, Pentameric, Glycine, Receptor, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9pky__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9pky__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9pky__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.39 Å
Rg (electron density)	38.97 Å
Total Rg	39.31 Å
Atom count	14301
Residues	1698
Excluded volume	259640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9pky__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Glycine receptor, alpha 1
Molecular weight formula_weight	52537.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,C,B
Atom count atom_count	14301

MFALGIYLWETIVFFSLAASQQAAARKAASPMPPSEFLDKLMGKVSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARQHKELLRFQRRRRHLKEDEAGDGRFSFAAYGMGPACLQAKDGMAIKGNNNNAPTSTNPPEKTVEEMRKLFISRAKRIDTVSRVAFPLVFLIFNIFYWITYKIIRSEDIHKQLVPRGSHHHHHHHH

Source Source

Source organism organism	Danio rerio
Common name common_name	zebrafish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 2 Entity 2 polymer

Description description	Glycine receptor beta subunit 2
Molecular weight formula_weight	65820.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MKALKVIFMLLIICLWMEGGFTKEKSAKKWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKENLYFQGEKSAKKGKKKGKQVYCPSQLSSEDLARVPANSTSNILNKLLITYDPRIRPNFKGIPVEDRVNIFINSFGSIQETTMDYRVNIFLRQRWNDPRLRLPQDFKSDSLTVDPKMFKCLWKPDLFFANEKSANFHDVTQENILLFIFRNGDVLISMRLSVTLSCPLDLTLFPMDTQRCKMQLESFGYTTDDLQFMWQSGDPVQMDEIALPQFDIKQEDIEYGNCTKYYAGTGYYTCVEVIFTLRRQVGFYMMGVYAPTLLIVVLSWLSFWINPDASAARVPLGILSVLSLSSECTSLASELPKVSYVKAIDIWLIACLLFGFASLVEYAVVQVMLNSPKLLEAERAKIATKEKAEGKTPAKNTINGMGSTPIHVSTLQVTETRCKKVCTSKSDLRTNDFSIVGSLPRDFELSNFDCYGKPIEVGSAFSKSQAKNNKKPPPPKPVIPSAAKRIDLYARALFPFSFLFFNVIYWSVYLENLYFQGTETSQVAPA

Source Source

Source organism organism	Danio rerio
Common name common_name	zebrafish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	STRYCHNINE
Molecular weight formula_weight	334.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	875.1 kDa
Source method src_method	syn
Copy count entity_count	5

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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	2.890 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.89 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	93904

Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 2000 nM ivermectin

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

Glycine receptor, alpha 1

State in the Current Structure

Other States of the Same Protein in the Database

Glycine receptor beta subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pky__assembly_1__model_1

9pky__assembly_1__model_1 | I(q)

9pky__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 2000 nM ivermectin

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

Glycine receptor, alpha 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Glycine receptor beta subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pky__assembly_1__model_1

9pky__assembly_1__model_1 | I(q)

9pky__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)