SAXSdb — 5owc

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

Group 10 secretory phospholipase A2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]propanoic acid × 1 DIMETHYL SULFOXIDE × 2 DI(HYDROXYETHYL)ETHER × 4 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]propanoic acid × 1 DIMETHYL SULFOXIDE × 2 DI(HYDROXYETHYL)ETHER × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PA2GX_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 43–164 Author chain B； PDBConstruct 1–122； UniProt 43–164

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	5owc
Deposition date deposition_date	2017-08-31
Structure title title	Indole-2 carboxamides as selective secreted phospholipase A2 type X (sPLA2-X) inhibitors
Keywords keywords	Inhibitor, secreted, phospholipase, LIPID BINDING PROTEIN; LIPID BINDING 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.

5owc__assembly_2__model_1

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

Download this curve (.dat)

5owc__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5owc__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	15.03 Å
Rg (electron density)	14.30 Å
Total Rg	15.36 Å
Atom count	988
Residues	122
Excluded volume	17493 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5owc__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5owc__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 (6)

Entity 1 Entity 1 polymer

Description description	Group 10 secretory phospholipase A2
Molecular weight formula_weight	13529.4 kDa
EC 编号 ec_number	3.1.1.4
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	2119

GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKC

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 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]propanoic acid
Molecular weight formula_weight	392.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5owca_
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

Domain ID domain_id	d5owcb_
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 (2 domains)

Domain ID domain_id	5owcA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

Domain ID domain_id	5owcB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

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Unit-cell length a length_a	27.850 Å
Unit-cell length b length_b	86.510 Å
Unit-cell length c length_c	103.440 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1846
R_work r_work	0.1827
R_free r_free	0.2208

Indole-2 carboxamides as selective secreted phospholipase A2 type X (sPLA2-X) inhibitors

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

Group 10 secretory phospholipase A2

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

5owc__assembly_2__model_1

5owc__assembly_2__model_1 | I(q)

5owc__assembly_2__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Indole-2 carboxamides as selective secreted phospholipase A2 type X (sPLA2-X) inhibitors

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

Group 10 secretory phospholipase A2

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

5owc__assembly_2__model_1

5owc__assembly_2__model_1 | I(q)

5owc__assembly_2__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)