SAXSdb — 8pih

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

Phospholipase A2

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	nanobody AM1-4 × 1 nanobdoy AM1-1 × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PA2_APIME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 35–167

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	8pih
Deposition date deposition_date	2023-06-21
Structure title title	Structure of Api m1 in complex with two nanobodies
Keywords keywords	allergen, antibody, nanobody; ALLERGEN
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.

8pih__assembly_1__model_1

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

Download this curve (.dat)

8pih__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8pih__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.65 Å
Rg (electron density)	25.60 Å
Total Rg	26.18 Å
Atom count	5452
Residues	361
Excluded volume	48924 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8pih__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	Phospholipase A2
Molecular weight formula_weight	15161.2 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	5709

IYPGTLWCGHGNKSSGPNELGRFKHTDACCRTHDMCPDVMSAGESKHGLTNTASHTRLSCDCDDKFYDCLKNSADTISSYFVGKMYFNLIDTKCYKLEHPVTGCGERTEGRCLHYTVDKSKPKVYQWFDLRKY

Entity 2 Entity 2 polymer

Description description	nanobody AM1-4
Molecular weight formula_weight	13607.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLVESGGGLVQAGGSLRLSCAASGRTFSRYAMGWFRQAPGKEREFVSAISGSGGFTDYADSVKGRFTISRDNAKSTVYLRMSSLKPEDTAVYYCAAEGSRGSSTRLDARGTYDYWGQGTQVTVSS

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	nanobdoy AM1-1
Molecular weight formula_weight	12889.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QVQLVETGGGLVQAGGSLRLSCATSGTIFSRATMAWYRQTPGKQREWVTTITTSGNTNYADSVKGRFTISRDNAESTLYLQMNSLKPEDTAVYYCNAQFLSSRTNYWGKGTQVTVSSG

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	200

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Unit-cell length a length_a	133.960 Å
Unit-cell length b length_b	51.330 Å
Unit-cell length c length_c	73.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	120.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	42.020 Å
R factor r_factor	0.1725
R_work r_work	0.1711
R_free r_free	0.2019

Structure of Api m1 in complex with two nanobodies

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8pih__assembly_1__model_1

8pih__assembly_1__model_1 | I(q)

8pih__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Structure of Api m1 in complex with two nanobodies

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8pih__assembly_1__model_1

8pih__assembly_1__model_1 | I(q)

8pih__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)