SAXSdb — 3jql

▼

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

Acidic phospholipase A2 3 (Fragment)

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Amyloid Beta Peptide × 1 CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PA2A3_NAJSG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–119； UniProt 8–126

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3jql
Deposition date deposition_date	2009-09-07
Structure title title	Crystal Structure of the Complex Formed Between Phospholipase A2 and a Hexapeptide Fragment of Amyloid Beta Peptide, Lys-Leu-Val-Phe-Phe-Ala at 1.2 A Resolution
Keywords keywords	PHOSPHOLIPASE A2, HEXAPEPTIDE, AMYLOID BETA, HYDROLASE, Disulfide bond, Lipid degradation, Metal-binding, Secreted; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3jql__assembly_1__model_1

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

Download this curve (.dat)

3jql__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3jql__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.12 Å
Rg (electron density)	13.99 Å
Total Rg	15.04 Å
Atom count	961
Residues	125
Excluded volume	16758 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3jql__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Acidic phospholipase A2 3 (Fragment)
Molecular weight formula_weight	13128.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1110

NLYQFKNMIQCTVPSRSWADFADYGCYCGKGGSGTPVDDLDRCCQTHDNCYNEAENISGCRPYFKTYSYECTQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDANYNIDLKARCN

Entity 2 Entity 2 polymer

Description description	Amyloid Beta Peptide
Molecular weight formula_weight	724.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KLVFFA

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
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	149

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3jqla_
Class class	a — All alpha proteins
Fold Fold fold	a.133 — Phospholipase A2, PLA2
Superfamily Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
Family Family family	a.133.1.2 — Vertebrate phospholipase A2

CATH v4.4 (1 domains)

Domain ID domain_id	3jqlA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

▶

Unit-cell length a length_a	42.023 Å
Unit-cell length b length_b	42.023 Å
Unit-cell length c length_c	64.146 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	42.000 Å
R factor r_factor	0.1866
R_work r_work	0.1808
R_free r_free	0.1928

Crystal Structure of the Complex Formed Between Phospholipase A2 and a Hexapeptide Fragment of Amyloid Beta Peptide, Lys-Leu-Val-Phe-Phe-Ala at 1.2 A Resolution

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

Acidic phospholipase A2 3 (Fragment)

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

3jql__assembly_1__model_1

3jql__assembly_1__model_1 | I(q)

3jql__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

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 Complex Formed Between Phospholipase A2 and a Hexapeptide Fragment of Amyloid Beta Peptide, Lys-Leu-Val-Phe-Phe-Ala at 1.2 A Resolution

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

Acidic phospholipase A2 3 (Fragment)

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

3jql__assembly_1__model_1

3jql__assembly_1__model_1 | I(q)

3jql__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

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)