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5neb

Structure of GluK1 ligand-binding domain (S1S2) in complex with LM-12b at 2.05 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

UniProt P22756

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 SULFATE ION × 3 CHLORIDE ION × 2 GLYCEROL × 1 (3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic acid × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 SULFATE ION × 5 CHLORIDE ION × 2 GLYCEROL × 1 (3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic acid × 1 ACETATE ION × 1 water × 1 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 P22756-2
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_id5neb
Deposition date deposition_date2017-03-10
Structure title titleStructure of GluK1 ligand-binding domain (S1S2) in complex with LM-12b at 2.05 A resolution
Keywords keywordsIONOTROPIC GLUTAMATE RECEPTOR, KAINATE RECEPTOR, LIGAND-BINDING DOMAIN, GLUK1, GLUR5, AGONIST, MEMBRANE PROTEIN; MEMBRANE 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.

5neb__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5neb__assembly_2__model_1 | I(q)

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

5neb__assembly_2__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）19.82 Å
Rg (electron density)18.63 Å
Total Rg19.64 Å
Atom count2053
Residues251
Excluded volume36733 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5neb__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5neb__assembly_2__model_1 monomeric （1） 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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5neba1
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_idd5neba2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5nebb1
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_idd5nebb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id5nebA01
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_id5nebA02
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_id5nebB01
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_id5nebB02
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 (1)