SAXSdb — 5el2

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

AGAP003309-PA

Anopheles gambiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 1 Icaridin × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8I8T0_ANOGA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 20–144 Author chain B； PDBConstruct 1–125； UniProt 20–144

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	5el2
Deposition date deposition_date	2015-11-04
Structure title title	Crystal structure of Odorant Binding Protein 1 from Anopheles gambiae (AgamOBP1) with Icaridin (butan-2-yl 2-(2-hydroxyethyl)piperidine-1-carboxylate)
Keywords keywords	;TRANSPORT PROTEIN, INSECT ODORANT BINDING PROTEIN, OBP1, AGAMOBP1, OLFACTION, ICARIDIN, butan-2-yl 2-(2-hydroxyethyl)piperidine-1-carboxylate ;; TRANSPORT 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.

5el2__assembly_1__model_1

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

Download this curve (.dat)

5el2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5el2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.59 Å
Rg (electron density)	20.81 Å
Total Rg	21.65 Å
Atom count	2099
Residues	250
Excluded volume	37460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5el2__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	AGAP003309-PA
Molecular weight formula_weight	14547.6 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	2654

DTTPRRDAEYPPPELLEALKPLHDICLGKTGVTEEAIKKFSDEEIHEDEKLKCYMNCLFHEAKVVDDNGDVHLEKLHDSLPSSMHDIAMHMGKRCLYPEGETLCDKAFWLHKCWKQSDPKHYFLV

Source Source

Source organism organism	Anopheles gambiae
Common name common_name	African malaria mosquito
NCBI taxonomy ID ncbi_taxonomy_id	7165
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	Icaridin
Molecular weight formula_weight	229.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	307

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5el2a_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.2 — Insect pheromone/odorant-binding proteins
Family Family family	a.39.2.0 — automated matches

Domain ID domain_id	d5el2b_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.2 — Insect pheromone/odorant-binding proteins
Family Family family	a.39.2.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5el2A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	20 — Pheromone/general odorant binding protein domain

Domain ID domain_id	5el2B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	20 — Pheromone/general odorant binding protein domain

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Unit-cell length a length_a	29.984 Å
Unit-cell length b length_b	68.476 Å
Unit-cell length c length_c	61.675 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	60.810 Å
R factor r_factor	0.1796
R_work r_work	0.1775
R_free r_free	0.2209

Crystal structure of Odorant Binding Protein 1 from Anopheles gambiae (AgamOBP1) with Icaridin (butan-2-yl 2-(2-hydroxyethyl)piperidine-1-carboxylate)

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

AGAP003309-PA

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

5el2__assembly_1__model_1

5el2__assembly_1__model_1 | I(q)

5el2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Odorant Binding Protein 1 from Anopheles gambiae (AgamOBP1) with Icaridin (butan-2-yl 2-(2-hydroxyethyl)piperidine-1-carboxylate)

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

AGAP003309-PA

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

5el2__assembly_1__model_1

5el2__assembly_1__model_1 | I(q)

5el2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)