SAXSdb — 1tdv

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

Phospholipase A2 VRV-PL-VIIIa

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	YWAAAA × 1 SULFATE ION × 6 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PA28_DABRP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 1–121

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	1tdv
Deposition date deposition_date	2004-05-24
Structure title title	Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution
Keywords keywords	NON-SPECIFIC, YWAAAA COMPLEX, PHOSPHOLIPASE A2, hydrolase; HYDROLASE
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.

1tdv__assembly_1__model_1

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

Download this curve (.dat)

1tdv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tdv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.83 Å
Rg (electron density)	14.92 Å
Total Rg	16.06 Å
Atom count	1020
Residues	127
Excluded volume	17955 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tdv__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	Phospholipase A2 VRV-PL-VIIIa
Molecular weight formula_weight	13629.8 kDa
EC 编号 ec_number	3.1.1.4
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	1167

SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC

Entity 2 Entity 2 polymer

Description description	YWAAAA
Molecular weight formula_weight	651.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

YWAAAA

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1tdva_
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	1tdvA00
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	52.290 Å
Unit-cell length b length_b	52.290 Å
Unit-cell length c length_c	47.810 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	51.990 Å
R factor r_factor	0.1803
R_work r_work	0.1789
R_free r_free	0.2061

Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution

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

Phospholipase A2 VRV-PL-VIIIa

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

1tdv__assembly_1__model_1

1tdv__assembly_1__model_1 | I(q)

1tdv__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)

Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution

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

Phospholipase A2 VRV-PL-VIIIa

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

1tdv__assembly_1__model_1

1tdv__assembly_1__model_1 | I(q)

1tdv__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)