SAXSdb — 2q2j

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

Phospholipase A2 homolog 1

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–121 Chain B； UniProt 1–121	Not recorded	SO4 SULFATE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；0.1M Tris HCl, 30% PEG 4000, 0.2M lithium sulfate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.258

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 2Q2J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OK9 PrTX-I-BPB Deposited 2007-01-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	PBP p-Bromophenacyl bromide × 2 IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；23% PEG 4000, 20% 2-propanol, 0.1M sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.34 Å R-free 0.252
3QNL Crystal structure of PrTX-I complexed to Rosmarinic Acid Deposited 2011-02-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 8 ROA (2R)-3-(3,4-dihydroxyphenyl)-2-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}propanoic acid × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20% PEG 4000, sodium citrate pH 5.6, 20% 2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.77 Å R-free 0.218
4YU7 Crystal structure of Piratoxin I (PrTX-I) complexed to caffeic acid Deposited 2015-03-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 3 DHC CAFFEIC ACID × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；291 K；PEG4000, Tris HCl pH 8.1, lithium sulfate.	Resolution 1.65 Å R-free 0.229
4YZ7 Crystal structure of Piratoxin I (PrTX-I) complexed to aristolochic acid Deposited 2015-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 5 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 9AR 9-HYDROXY ARISTOLOCHIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；291 K；PEG 4000, Tris HCl pH 8.1 and lithium sulfate	Resolution 1.96 Å R-free 0.235
8DND Crystal structure of Bothrops pirajai Piratoxin-I (PrTX-I) and synthetic inhibitor Varespladib (LY315920) Deposited 2022-07-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	VRD ({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid × 3 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% w/v PEG 4000, 0.1 M Tris HCl pH 8.5 and 0.2 M lithium sulfate	Resolution 2.02 Å R-free 0.217
9Z5Y Crystal structure of Bothrops pirajai myotoxin I PrTX-I complexed with inhibitor AZD2716 Deposited 2025-11-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	A1C06 (2R)-3-[(1M)-5'-benzyl-2'-carbamoyl[1,1'-biphenyl]-3-yl]-2-methylpropanoic acid × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；PEG 4000, Tris HCl, Lithium Sulfate	Resolution 2.75 Å R-free 0.269

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

View Construct and Data Evidence

UniProt name	PA21B_BOTPI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 1–121 Author chain B； 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	2q2j
Deposition date deposition_date	2007-05-28
Structure title title	Crystal structure of PrTX-I, a PLA2 homolog from Bothrops pirajai
Keywords keywords	myotoxin, PLA2 like, Lys49-PLA2, phospholipase A2, TOXIN; TOXIN
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	19.18 Å
Radius of gyration Rg (electron density) rg_electron	18.35 Å
Forward intensity I(0) i0	14445900.00
Molecular weight molecular_weight	26991.0 kDa
Excluded volume excluded_volume	33135 Å³
Envelope volume envelope_volume	37924 Å³
Hydration-shell volume shell_volume	17626 Å³
Envelope diameter envelope_diameter	68.6 Å
Shell Rg shell_rg	24.30 Å
Envelope Rg envelope_rg	18.41 Å
Shape Rg shape_rg	18.33 Å
Total Rg total_rg	19.24 Å
Total atoms total_atoms	1869
Residues n_residues	242
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	69.5 Å
Rg (real space) rg_real	19.10 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.4450e+07
I(0) uncertainty (real space) i0_real_error	1.7280e+05
Rg (reciprocal space) rg_reciprocal	19.11 Å
I(0) (reciprocal space) i0_reciprocal	14450000.0000
Solution quality estimate total_estimate	0.7651
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.209
Kurtosis Kurtosis kurtosis	-0.296
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4395000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.666; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Phospholipase A2 homolog 1
Molecular weight formula_weight	13770.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2269

SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	400

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2q2ja_
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	d2q2jb_
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	2q2jA00
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	2q2jB00
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	55.883 Å
Unit-cell length b length_b	55.883 Å
Unit-cell length c length_c	127.913 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	31.990 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2580

fit	/app/data/saxs_computation/q2/2q2j/2q2j.fit
pddf	/app/data/pr_computation/q2/2q2j/2q2j.pr.out
profile	/app/data/saxs_computation/q2/2q2j/2q2j.dat

Crystal structure of PrTX-I, a PLA2 homolog from Bothrops pirajai

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

Phospholipase A2 homolog 1

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