SAXSdb — 3k6b

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

Beta-amyloid-like protein

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–239； UniProt 240–478

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	3k6b
Deposition date deposition_date	2009-10-08
Structure title title	X-ray crystal structure of the E2 domain of APL-1 from C. elegans, in complex with sucrose octasulfate (SOS)
Keywords keywords	;X-ray crystal structure, amyloid precursor protein, heparin binding, Alternative splicing, Amyloid, Developmental protein, Differentiation, Glycoprotein, Membrane, Neurogenesis, Transmembrane, CELL ADHESION ;; CELL ADHESION
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.

3k6b__assembly_1__model_1

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

Download this curve (.dat)

3k6b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3k6b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.78 Å
Rg (electron density)	26.72 Å
Total Rg	26.76 Å
Atom count	1741
Residues	218
Excluded volume	30424 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3k6b__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Beta-amyloid-like protein
Molecular weight formula_weight	28516.4 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	1775

SQDPYFKIANWTNEHDDFKKAEMRMDEKHRKKVDKVMKEWGDLETRYNEQKAKDPKGAEKFKSQMNARFQKTVSSLEEEHKRMRKEIEAVHEERVQAMLNEKKRDATHDYRQALATHVNKPNKHSVLQSLKAYIRAEEKDRMHTLNRYRHLLKADSKEAAAYKPTVIHRLRYIDLRINGTLAMLRDFPDLEKYVRPIAVTYWKDYRDEVSPDISVEDSELTPIIHDDEFSKNAKLDVKA

Source Source

Source organism organism	Caenorhabditis elegans
Common name common_name	nematode
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose
Molecular weight formula_weight	500.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3k6bA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	770 — Amyloid precursor protein, E2 domain

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Unit-cell length a length_a	97.314 Å
Unit-cell length b length_b	97.314 Å
Unit-cell length c length_c	67.462 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2620
R_work r_work	0.2620
R_free r_free	0.3090

X-ray crystal structure of the E2 domain of APL-1 from C. elegans, in complex with sucrose octasulfate (SOS)

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

Beta-amyloid-like protein

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

3k6b__assembly_1__model_1

3k6b__assembly_1__model_1 | I(q)

3k6b__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)

X-ray crystal structure of the E2 domain of APL-1 from C. elegans, in complex with sucrose octasulfate (SOS)

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

Beta-amyloid-like protein

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

3k6b__assembly_1__model_1

3k6b__assembly_1__model_1 | I(q)

3k6b__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)