SAXSdb — 9cmc

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

Ara h 2 allergen

Arachis hypogaea

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Fab 23P34 heavy chain × 1 Fab 23P34 light chain × 1 Fab 22S1 heavy chain × 1 Fab 22S1 light chain × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Fab 23P34 heavy chain × 1 Fab 23P34 light chain × 1 Fab 22S1 heavy chain × 1 Fab 22S1 light chain × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Fab 23P34 heavy chain × 1 Fab 23P34 light chain × 1 Fab 22S1 heavy chain × 1 Fab 22S1 light chain × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	Fab 23P34 heavy chain × 1 Fab 23P34 light chain × 1 Fab 22S1 heavy chain × 1 Fab 22S1 light chain × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A445BYI5_ARAHY
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 6–140； UniProt 26–160 Author chain J； PDBConstruct 6–140； UniProt 26–160 Author chain O； PDBConstruct 6–140； UniProt 26–160 Author chain T； PDBConstruct 6–140； UniProt 26–160

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	9cmc
Deposition date deposition_date	2024-07-14
Structure title title	Crystal structure of the peanut allergen Ara h 2 with two human derived Fab antibodies 22S1 and 23P34
Keywords keywords	allergy, antibody complex, peanut, ALLERGEN; 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.

9cmc__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9cmc__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9cmc__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	44.74 Å
Rg (electron density)	46.06 Å
Total Rg	45.94 Å
Atom count	6925
Residues	950
Excluded volume	121770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9cmc__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9cmc__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9cmc__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9cmc__assembly_4__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Fab 23P34 heavy chain
Molecular weight formula_weight	24353.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F,K,P
Atom count atom_count	25639

QVQLVESGGLVVQPGGSLRLSCEASGFTFDDYTMHWVRQSPQKGLEWVSLIRWDGSRTEYADSVKGRFTISRDNSKNSLYLQMNTLRADDSAFYFCVKDGGLRYFDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Fab 23P34 light chain
Molecular weight formula_weight	23799.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G,L,Q

DVVMTQSPLSLPVTPGEPASISCRSSQSLLHSNGIHYLDWYLQKPGQSPQLLIYLGSKRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSLQTFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Fab 22S1 heavy chain
Molecular weight formula_weight	24291.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H,M,R

QVQLVQSGGGLVKPGGSLRLSCTASGFSFSDSYMSWIRQAPGKGLEWLTYISGSGEIISYADSVKGRFTISRDNAKKSVYLQMDSLRAEDTAVYYCARPSDYFETSEELDWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 4 Entity 4 polymer

Description description	Fab 22S1 light chain
Molecular weight formula_weight	23402.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I,N,V

EIVMTQSPSSLSASVGDRVTITCRASQSISTYLNWYQQKPGKAPNLLIYAASSLHSGVPSRFRGSGSGTDFTLTITSLQPDDFATYYCHQSYSAPRTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 5 Entity 5 polymer

Description description	Ara h 2 allergen
Molecular weight formula_weight	16417.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J,O,T

GSAAAELQGDRRCQSQLERANLRPCEQHLMQKIQRDEDSYERDPYSPSQDPYSPSPYDRRGAGSSQHQERCCNELNEFENNQRCMCEALQQIMENQSDRLQGRQQEQQFKRELRNLPQQCGLRAPQRCDLDVESGGRDRY

Source Source

Source organism organism	Arachis hypogaea
Common name common_name	peanut
NCBI taxonomy ID ncbi_taxonomy_id	3818
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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Unit-cell length a length_a	90.906 Å
Unit-cell length b length_b	165.009 Å
Unit-cell length c length_c	164.642 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	49.530 Å
R factor r_factor	0.2142
R_work r_work	0.2134
R_free r_free	0.2531

Crystal structure of the peanut allergen Ara h 2 with two human derived Fab antibodies 22S1 and 23P34

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

Ara h 2 allergen

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

9cmc__assembly_3__model_1

9cmc__assembly_3__model_1 | I(q)

9cmc__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of the peanut allergen Ara h 2 with two human derived Fab antibodies 22S1 and 23P34

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

Ara h 2 allergen

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

9cmc__assembly_3__model_1

9cmc__assembly_3__model_1 | I(q)

9cmc__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 water

7. Citations (1)