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4ymb

Structure of the ligand-binding domain of GluK1 in complex with the antagonist CNG10111

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1

Rattus norvegicus

UniProt P22756

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 (3R,4S)-3-(3-carboxyphenyl)-4-propyl-L-proline × 2 ACETATE ION × 4 CHLORIDE ION × 4 DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1txf 2f34 2f34 2f35 2f35 3gba 3gba 3gba 3gba 3gbb 3gbb 5neb

13 assemblies; showing the first 12

Homodimer
1vso 1ycj 2f34 2f34 2f35 2f35 2ojt 2ojt 2pbw 2qs1 2qs1 2qs2

38 assemblies; showing the first 12

Homotetramer
2f36 4e0x

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name GRIK1_RAT
Isoform P22756-3
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–116； UniProt 445–559 Author chain A； PDBConstruct 119–257； UniProt 682–820 Author chain B； PDBConstruct 2–116； UniProt 445–559 Author chain B； PDBConstruct 119–257； UniProt 682–820

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_id4ymb
Deposition date deposition_date2015-03-06
Structure title titleStructure of the ligand-binding domain of GluK1 in complex with the antagonist CNG10111
Keywords keywordsIonotropic glutamate receptor, kainate receptor GluK1, ligand-binding domain, antagonist, signaling protein, fusion protein; SIGNALING PROTEIN
Experimental Method methodX-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.

4ymb__assembly_1__model_1

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

Download this curve (.dat)

4ymb__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4ymb__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）25.12 Å
Rg (electron density)23.86 Å
Total Rg24.79 Å
Atom count8256
Residues507
Excluded volume74024 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4ymb__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)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4ymba_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.0 — automated matches
Domain ID domain_idd4ymbb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like

CATH v4.4 (4 domains)

Domain ID domain_id4ymbA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id4ymbA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id4ymbB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id4ymbB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
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7. Citations (2)