SAXSdb — 4yu7

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

Basic phospholipase A2 homolog piratoxin-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	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

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 4YU7	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
2Q2J Crystal structure of PrTX-I, a PLA2 homolog from Bothrops pirajai Deposited 2007-05-28	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 × 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
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
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	PA2H1_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	4yu7
Deposition date deposition_date	2015-03-18
Structure title title	Crystal structure of Piratoxin I (PrTX-I) complexed to caffeic acid
Keywords keywords	Phospholipase A2 Phospholipase A2-like Bothrops snake venom inhibitor, 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	19.35 Å
Radius of gyration Rg (electron density) rg_electron	18.41 Å
Forward intensity I(0) i0	15266700.00
Molecular weight molecular_weight	28212.0 kDa
Excluded volume excluded_volume	34747 Å³
Envelope volume envelope_volume	40684 Å³
Hydration-shell volume shell_volume	18570 Å³
Envelope diameter envelope_diameter	67.5 Å
Shell Rg shell_rg	24.65 Å
Envelope Rg envelope_rg	18.45 Å
Shape Rg shape_rg	18.41 Å
Total Rg total_rg	19.29 Å
Total atoms total_atoms	1957
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	65.3 Å
Rg (real space) rg_real	19.23 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.5270e+07
I(0) uncertainty (real space) i0_real_error	2.0100e+05
Rg (reciprocal space) rg_reciprocal	19.25 Å
I(0) (reciprocal space) i0_reciprocal	15270000.0000
Solution quality estimate total_estimate	0.7934
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.138
Kurtosis Kurtosis kurtosis	-0.353
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5090000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Basic phospholipase A2 homolog piratoxin-1
Molecular weight formula_weight	13754.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	2246

SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKLYRYHLKPFCKKADDC

Entity 2 Entity 2 non-polymer

Description description	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Molecular weight formula_weight	354.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CAFFEIC ACID
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	289

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4yu7a_
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	d4yu7b_
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	4yu7A00
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	4yu7B00
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 (2)

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Unit-cell length a length_a	39.233 Å
Unit-cell length b length_b	72.082 Å
Unit-cell length c length_c	44.644 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.647 Å
Low-resolution limit resolution_low	37.341 Å
R factor r_factor	0.1847
R_work r_work	0.1823
R_free r_free	0.2287

fit	/app/data/saxs_computation/yu/4yu7/4yu7.fit
pddf	/app/data/pr_computation/yu/4yu7/4yu7.pr.out
profile	/app/data/saxs_computation/yu/4yu7/4yu7.dat

Crystal structure of Piratoxin I (PrTX-I) complexed to caffeic acid

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

Basic phospholipase A2 homolog piratoxin-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