SAXSdb — 9gvn

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

Interleukin-5

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 20–134 Chain B； UniProt 20–134	Not recorded	Fab heavy chain × 2 Fab light chain × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；Morpheus EDO_P8K, Morpheus Carboxylic acids, Morpheus buffer system 2	Resolution 1.93 Å R-free 0.209

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 9GVN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HUL A NOVEL DIMER CONFIGURATION REVEALED BY THE CRYSTAL STRUCTURE AT 2.4 ANGSTROMS RESOLUTION OF HUMAN INTERLEUKIN-5 Deposited 1995-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–131（108 aa） Chain B 24–131（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.369
3QT2 Structure of a cytokine ligand-receptor complex Deposited 2011-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 19–134（116 aa） Chain D 19–134（116 aa）	Not recorded	BGC beta-D-glucopyranose × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.264
3QT2 Structure of a cytokine ligand-receptor complex Deposited 2011-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 19–134（116 aa） Chain F 19–134（116 aa）	Not recorded	BGC beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.264
3VA2 Crystal structure of human Interleukin-5 in complex with its alpha receptor Deposited 2011-12-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 23–134（112 aa） Fragment：UNP residues 23-134 Chain B 23–134（112 aa） Fragment：UNP residues 23-134	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；0.1M Na HEPES, 22% (v/v) PEG 4000, 2% i-Propanol, 6% (w/v) 1,6-Hexanediol , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.276
8TLD Structure of the IL-5 Signaling Complex Deposited 2023-07-26	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 20–134（115 aa） Chain D 20–134（115 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IL5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–115； UniProt 20–134 Author chain B； PDBConstruct 1–115； UniProt 20–134

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	9gvn
Deposition date deposition_date	2024-09-25
最后修订 last_revision	2026-01-14
Structure title title	DEPEMOKIMAB FAB IN COMPLEX WITH INTERLEUKIN 5
Keywords keywords	IL-5, ANTIBODY, COMPLEX, EPITOPE, CYTOKINE, GLYCOPROTEIN, IMMUNOGLOBULIN FOLD, IMMUNE SYSTEM; IMMUNE SYSTEM
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	41.42 Å
Radius of gyration Rg (electron density) rg_electron	41.25 Å
Forward intensity I(0) i0	217790000.00
Molecular weight molecular_weight	120300.0 kDa
Excluded volume excluded_volume	150560 Å³
Envelope volume envelope_volume	209830 Å³
Hydration-shell volume shell_volume	42650 Å³
Envelope diameter envelope_diameter	133.5 Å
Shell Rg shell_rg	46.15 Å
Envelope Rg envelope_rg	40.77 Å
Shape Rg shape_rg	41.21 Å
Total Rg total_rg	41.61 Å
Total atoms total_atoms	8460
Residues n_residues	1092
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	131.7 Å
Rg (real space) rg_real	41.51 Å
Rg uncertainty (real space) rg_real_error	1.23 Å
I(0) (real space) i0_real	2.1780e+08
I(0) uncertainty (real space) i0_real_error	3.7580e+06
Rg (reciprocal space) rg_reciprocal	41.43 Å
I(0) (reciprocal space) i0_reciprocal	217800000.0000
Solution quality estimate total_estimate	0.8265
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.1 Å
Skewness Skewness skewness	0.256
Kurtosis Kurtosis kurtosis	-0.778
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16320000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Interleukin-5
Molecular weight formula_weight	13166.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9240

IPTEIPTSALVKETLALLSTHRTLLIANETLRIPVPVHKNHQLCTEEIFQGIGTLESQTVQGGTVERLFKNLSLIKKYIDGQKKKCGEERRRVNQFLDYLQEFLGVMNTEWIIES

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Drosophila

Entity 2 Entity 2 polymer

Description description	Fab heavy chain
Molecular weight formula_weight	23971.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E

QVTLRESGPALVKPTQTLTLTCTVSGFSLTGSSVHWVRQPPGKGLEWLGVIWASGGTDYNSALMSRLSISKDTSRNQVVLTMTNMDPVDTATYYCARDPPSGLLRLDYWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Fab light chain
Molecular weight formula_weight	23969.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F

DIVMTQSPDSLAVSLGERATINCKSSQSLLNSGNQKNYLAWYQQKPGQPPKLLIYGASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQNVHSFPFTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1057.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	772

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8. Citations (1)

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Unit-cell length a length_a	86.684 Å
Unit-cell length b length_b	65.870 Å
Unit-cell length c length_c	193.754 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.62 °
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	1.933 Å
Low-resolution limit resolution_low	192.460 Å
R factor r_factor	0.1846
R_work r_work	0.1833
R_free r_free	0.2087

fit	/app/data/saxs_computation/gv/9gvn/9gvn.fit
pddf	/app/data/pr_computation/gv/9gvn/9gvn.pr.out
profile	/app/data/saxs_computation/gv/9gvn/9gvn.dat

DEPEMOKIMAB FAB IN COMPLEX WITH INTERLEUKIN 5

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

Interleukin-5

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

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)