SAXSdb — 9z5y

▼

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

Basic phospholipase A2 homolog piratoxin-1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;(2R)-3-[(1M)-5'-benzyl-2'-carbamoyl[1,1'-biphenyl]-3-yl]-2-methylpropanoic acid ; × 2 SULFATE ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9z5y
Deposition date deposition_date	2025-11-13
Last revision last_revision	2026-04-22
Structure title title	Crystal structure of Bothrops pirajai myotoxin I PrTX-I complexed with inhibitor AZD2716
Keywords keywords	Bothrops pirajai, PrTX-I, Piratoxin I, Phospholipase A2-like, AZD2716, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

9z5y__assembly_1__model_1

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

Download this curve (.dat)

9z5y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9z5y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.46 Å
Rg (electron density)	18.56 Å
Total Rg	19.52 Å
Atom count	1940
Residues	242
Excluded volume	34124 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9z5y__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

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	A,B
Atom count atom_count	1973

SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKLYRYHLKPFCKKADDC

Entity 2 Entity 2 non-polymer

Description description	;(2R)-3-[(1M)-5'-benzyl-2'-carbamoyl[1,1'-biphenyl]-3-yl]-2-methylpropanoic acid ;
Molecular weight formula_weight	373.4 kDa
Source method src_method	syn
Copy count entity_count	2

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	33

▶

Unit-cell length a length_a	52.135 Å
Unit-cell length b length_b	61.533 Å
Unit-cell length c length_c	89.720 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	2.750 Å
Low-resolution limit resolution_low	45.077 Å
R factor r_factor	0.2439
R_work r_work	0.2426
R_free r_free	0.2691

Crystal structure of Bothrops pirajai myotoxin I PrTX-I complexed with inhibitor AZD2716

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9z5y__assembly_1__model_1

9z5y__assembly_1__model_1 | I(q)

9z5y__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of Bothrops pirajai myotoxin I PrTX-I complexed with inhibitor AZD2716

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9z5y__assembly_1__model_1

9z5y__assembly_1__model_1 | I(q)

9z5y__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)