SAXSdb — 3c5t

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

Glucagon-like peptide 1 receptor

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Exendin-4 × 1 （P26349） decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLP1R_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 24–145

Exendin-4

OrganismNot specified

UniProt P26349

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Glucagon-like peptide 1 receptor × 1 （P43220） decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EXE4_HELSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–31； UniProt 56–86

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	3c5t
Deposition date deposition_date	2008-02-01
Structure title title	Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain
Keywords keywords	;ligand-bound G protein-coupled receptor extracellular domain, G-protein coupled receptor, Glycoprotein, Membrane, Transducer, Transmembrane, Amidation, Cleavage on pair of basic residues, Secreted, Signaling protein-Signaling protein COMPLEX ;; Signaling protein/Signaling 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.

3c5t__assembly_1__model_1

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

Download this curve (.dat)

3c5t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c5t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.91 Å
Rg (electron density)	16.06 Å
Total Rg	17.21 Å
Atom count	1088
Residues	129
Excluded volume	19152 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c5t__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 (4)

Entity 1 Entity 1 polymer

Description description	Glucagon-like peptide 1 receptor
Molecular weight formula_weight	14325.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1214

RPQGATVSLWETVQKWREYRRQCQRSLTEDPPPATDLFCNRTFDEYACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLQKDNSSLPWRDLSECEESKRGERSSPEEQLLFLY

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Exendin-4
Molecular weight formula_weight	3373.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DLSKQMEEEAVRLFIEWLKNGGPSSGAPPPS

Entity 3 Entity 3 non-polymer

Description description	decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside
Molecular weight formula_weight	498.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3c5tb1
Class class	j — Peptides
Fold Fold fold	j.6 — Peptide hormones
Superfamily Superfamily superfamily	j.6.1 — Peptide hormones
Family Family family	j.6.1.1 — Peptide hormones

CATH v4.4 (1 domains)

Domain ID domain_id	3c5tA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1240 — Hormone receptor fold
Homologous superfamily homologous superfamily	10 — GPCR, family 2, extracellular hormone receptor domain

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Unit-cell length a length_a	75.910 Å
Unit-cell length b length_b	75.910 Å
Unit-cell length c length_c	87.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	36.500 Å
R factor r_factor	0.2050
R_work r_work	0.2033
R_free r_free	0.2381

Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain

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

Glucagon-like peptide 1 receptor

State in the Current Structure

Other States of the Same Protein in the Database

Exendin-4

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

3c5t__assembly_1__model_1

3c5t__assembly_1__model_1 | I(q)

3c5t__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain

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

Glucagon-like peptide 1 receptor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exendin-4

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

3c5t__assembly_1__model_1

3c5t__assembly_1__model_1 | I(q)

3c5t__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)