8r36

Crystal structure of the Gluk1 ligand-binding domain in complex with kainate and BPAM538 at 1.90 A resolution

Method: X-RAY DIFFRACTION

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

Glutamate receptor ionotropic, kainate 1

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE × 2 SULFATE ION × 4 CHLORIDE ION × 8 GLYCEROL × 4 4-cyclopropyl-7-(3-methoxyphenoxy)-2,3-dihydro-1$l^{6},2,4-benzothiadiazine 1,1-dioxide × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GRIK1_RAT
Isoform	P22756-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–116； UniProt 430–544 Author chain A； PDBConstruct 119–257； UniProt 667–805 Author chain B； PDBConstruct 2–116； UniProt 430–544 Author chain B； PDBConstruct 119–257； UniProt 667–805

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	8r36
Deposition date deposition_date	2023-11-08
Structure title title	Crystal structure of the Gluk1 ligand-binding domain in complex with kainate and BPAM538 at 1.90 A resolution
Keywords keywords	IONOTROPIC GLUTAMATE RECEPTOR, GLUK1 LIGAND-BINDING DOMAIN, MEMBRANE PROTEIN, POSITIVE ALLOSTERIC MODULATOR, KAINATE; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

8r36__assembly_1__model_1

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

Download this curve (.dat)

8r36__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8r36__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.18 Å
Rg (electron density)	23.81 Å
Total Rg	24.79 Å
Atom count	4156
Residues	508
Excluded volume	74637 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8r36__assembly_1__model_1`	dimeric （2）	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 (7)

Entity 1 Entity 1 polymer

Description description	Glutamate receptor ionotropic, kainate 1
Molecular weight formula_weight	29108.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4586

GANRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
Molecular weight formula_weight	213.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	4-cyclopropyl-7-(3-methoxyphenoxy)-2,3-dihydro-1$l^{6},2,4-benzothiadiazine 1,1-dioxide
Molecular weight formula_weight	346.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	357

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Unit-cell length a length_a	71.485 Å
Unit-cell length b length_b	71.485 Å
Unit-cell length c length_c	232.902 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	46.370 Å
R factor r_factor	0.1659
R_work r_work	0.1642
R_free r_free	0.1993

Crystal structure of the Gluk1 ligand-binding domain in complex with kainate and BPAM538 at 1.90 A resolution

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

Glutamate receptor ionotropic, kainate 1

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

8r36__assembly_1__model_1

8r36__assembly_1__model_1 | I(q)

8r36__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of the Gluk1 ligand-binding domain in complex with kainate and BPAM538 at 1.90 A resolution

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

Glutamate receptor ionotropic, kainate 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8r36__assembly_1__model_1

8r36__assembly_1__model_1 | I(q)

8r36__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)