SAXSdb — 1a3d

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

PHOSPHOLIPASE A2

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–119	Not recorded	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；295.5 K；1.4M (NH4)2SO4, 1% PEG 400, AND 0.1M TRIS PH 7.5 AT 22.5 DEGREES C., temperature 295.5K	Resolution 1.80 Å R-free 0.230

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1A3D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A3F PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM Deposited 1998-01-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–119（119 aa） Chain B 1–119（119 aa） Chain C 1–119（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 295.5 K；UNBUFFERED 32.5% MONOMETHYL PEG 5K AND 0.17M SODIUM CITRATE AT 22.5 DEGREES C., temperature 295.5K	Resolution 2.65 Å R-free 0.260
1OWS Crystal structure of a C49 Phospholipase A2 from Indian cobra reveals carbohydrate binding in the hydrophobic channel Deposited 2003-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–118（118 aa） Chain B 4–119（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10mM Sodium Cacodylate, 2mM Zinc acetate, 25% Ethanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.256
1OWS Crystal structure of a C49 Phospholipase A2 from Indian cobra reveals carbohydrate binding in the hydrophobic channel Deposited 2003-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–118（118 aa） Chain B 4–119（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10mM Sodium Cacodylate, 2mM Zinc acetate, 25% Ethanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.256
1OWS Crystal structure of a C49 Phospholipase A2 from Indian cobra reveals carbohydrate binding in the hydrophobic channel Deposited 2003-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–118（118 aa） Chain B 4–119（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10mM Sodium Cacodylate, 2mM Zinc acetate, 25% Ethanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.256
1PSH CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM INDIAN COBRA REVEALS A TRIMERIC ASSOCIATION Deposited 1992-07-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–119（119 aa） Chain B 1–119（119 aa） Chain C 1–119（119 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
2WQ5 Non-antibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2. Deposited 2009-08-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–119（119 aa）	Not recorded	CA CALCIUM ION × 3 SO4 SULFATE ION × 3 MIY (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions 26% PEG 4000, 0.24M (NH4)2SO4	Resolution 1.65 Å R-free 0.230

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PA2_NAJNA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–119； UniProt 1–119

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	1a3d
Deposition date deposition_date	1998-01-20
Structure title title	PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM
Keywords keywords	PHOSPHOLIPASE, TRIMER, CALCIUM BINDING, ACTIVATOR SITE, CARBOXYLIC ESTER HYDROLASE; CARBOXYLIC ESTER HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	15.18 Å
Radius of gyration Rg (electron density) rg_electron	14.21 Å
Forward intensity I(0) i0	4145940.00
Molecular weight molecular_weight	13366.0 kDa
Excluded volume excluded_volume	16147 Å³
Envelope volume envelope_volume	18251 Å³
Hydration-shell volume shell_volume	11260 Å³
Envelope diameter envelope_diameter	48.2 Å
Shell Rg shell_rg	19.39 Å
Envelope Rg envelope_rg	14.49 Å
Shape Rg shape_rg	14.20 Å
Total Rg total_rg	15.23 Å
Total atoms total_atoms	929
Residues n_residues	119
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	49.7 Å
Rg (real space) rg_real	15.14 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	4.1460e+06
I(0) uncertainty (real space) i0_real_error	4.8160e+04
Rg (reciprocal space) rg_reciprocal	15.15 Å
I(0) (reciprocal space) i0_reciprocal	4146000.0000
Solution quality estimate total_estimate	0.8943
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.0 Å
Skewness Skewness skewness	0.273
Kurtosis Kurtosis kurtosis	-0.389
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	987000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a3da_
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	1a3dA00
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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8. Citations (1)

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Unit-cell length a length_a	69.240 Å
Unit-cell length b length_b	69.240 Å
Unit-cell length c length_c	69.240 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	12

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1750
R_work r_work	0.1750
R_free r_free	0.2300

Description description	PHOSPHOLIPASE A2
Molecular weight formula_weight	13357.9 kDa
EC 编号 ec_number	3.1.1.4
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1048

PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM

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

PHOSPHOLIPASE A2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	119

fit	/app/data/saxs_computation/a3/1a3d/1a3d.fit
pddf	/app/data/pr_computation/a3/1a3d/1a3d.pr.out
profile	/app/data/saxs_computation/a3/1a3d/1a3d.dat