SAXSdb — 1ax8

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

OBESITY PROTEIN

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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 22–167	Mutation：W100E	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 1.8M NA FORMATE, 100MM TRIS, PH 7.5	Resolution 2.40 Å R-free 0.283
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 22–167	Mutation：W100E	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 1.8M NA FORMATE, 100MM TRIS, PH 7.5	Resolution 2.40 Å R-free 0.283

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 1AX8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7Z3Q Crystal structure of the human leptin:LepR-CRH2 encounter complex to 3.6 A resolution. Deposited 2022-03-02	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 22–167（146 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Index screen HT #F1 0.2 M L-proline 0.1 M HEPES pH 7.5 10% PEG 3350 cryo: 25% PEG400	Resolution 3.62 Å R-free 0.305
7Z3Q Crystal structure of the human leptin:LepR-CRH2 encounter complex to 3.6 A resolution. Deposited 2022-03-02	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 22–167（146 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Index screen HT #F1 0.2 M L-proline 0.1 M HEPES pH 7.5 10% PEG 3350 cryo: 25% PEG400	Resolution 3.62 Å R-free 0.305
7Z3Q Crystal structure of the human leptin:LepR-CRH2 encounter complex to 3.6 A resolution. Deposited 2022-03-02	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 22–167（146 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Index screen HT #F1 0.2 M L-proline 0.1 M HEPES pH 7.5 10% PEG 3350 cryo: 25% PEG400	Resolution 3.62 Å R-free 0.305
8AVE Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric isoleucine GCN4 zipper (2:2 model) Deposited 2022-08-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 22–167（146 aa） Chain C 22–167（146 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.62 Å
8AVF Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric isoleucine GCN4 zipper (closed 3:3 model) Deposited 2022-08-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 22–167（146 aa） Chain C 22–167（146 aa） Chain E 22–167（146 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.45 Å
8AVO Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric isoleucine GCN4 zipper (open 3:3 model). Deposited 2022-08-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 22–167（146 aa） Chain C 22–167（146 aa） Chain E 22–167（146 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.84 Å
8K6Z NMR structure of human leptin Deposited 2023-07-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–167（146 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 5；Pressure 1 NMR sample composition 0.8 mM [U-13C; U-15N] leptin, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
8X80 Structure of leptin-LepR trimer with a small gap Deposited 2023-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–167（167 aa） Chain E 1–167（167 aa） Chain F 1–167（167 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
8X81 Structure of leptin-LepR trimer with a large gap Deposited 2023-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–167（167 aa） Chain E 1–167（167 aa） Chain F 1–167（167 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.77 Å
8X85 Structure of leptin-LepR dimer Deposited 2023-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–167（167 aa） Chain D 1–167（167 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
9PUO Neutralizing monoclonal antibody Fab fragment bound to leptin Deposited 2025-07-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 22–167（146 aa）	Mutation：W100E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Protein at 25 mg/ml in 20 mM Hepes pH 7.4 and 75 mM sodium chloride versus a reservoir with 18% PEG 8,000 and 20% glycerol.	Resolution 3.10 Å R-free 0.277
9PUO Neutralizing monoclonal antibody Fab fragment bound to leptin Deposited 2025-07-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 22–167（146 aa）	Mutation：W100E	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Protein at 25 mg/ml in 20 mM Hepes pH 7.4 and 75 mM sodium chloride versus a reservoir with 18% PEG 8,000 and 20% glycerol.	Resolution 3.10 Å R-free 0.277

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–146； UniProt 22–167

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	1ax8
Deposition date deposition_date	1997-10-31
Structure title title	Human obesity protein, leptin
Keywords keywords	HELICAL CYTOKINE, HEMATOPOIETIC FACTOR, DIABETES, OBESITY, CYTOKINE; CYTOKINE
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	15.56 Å
Radius of gyration Rg (electron density) rg_electron	14.32 Å
Forward intensity I(0) i0	3956410.00
Molecular weight molecular_weight	14311.0 kDa
Excluded volume excluded_volume	18065 Å³
Envelope volume envelope_volume	20078 Å³
Hydration-shell volume shell_volume	12113 Å³
Envelope diameter envelope_diameter	50.8 Å
Shell Rg shell_rg	19.82 Å
Envelope Rg envelope_rg	14.63 Å
Shape Rg shape_rg	14.33 Å
Total Rg total_rg	15.42 Å
Total atoms total_atoms	1003
Residues n_residues	130
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	50.9 Å
Rg (real space) rg_real	15.49 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	3.9560e+06
I(0) uncertainty (real space) i0_real_error	4.2530e+04
Rg (reciprocal space) rg_reciprocal	15.49 Å
I(0) (reciprocal space) i0_reciprocal	3956000.0000
Solution quality estimate total_estimate	0.6283
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.7 Å
Skewness Skewness skewness	0.216
Kurtosis Kurtosis kurtosis	-0.270
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	697700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ax8a_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.1 — Long-chain cytokines

CATH v4.4 (1 domains)

Domain ID domain_id	1ax8A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

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8. Citations (3)

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Unit-cell length a length_a	88.140 Å
Unit-cell length b length_b	88.140 Å
Unit-cell length c length_c	48.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2830

Description description	OBESITY PROTEIN
Molecular weight formula_weight	15984.3 kDa
Mutation mutation	W100E
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1074

Human obesity protein, leptin

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

OBESITY PROTEIN

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

fit	/app/data/saxs_computation/ax/1ax8/1ax8.fit
pddf	/app/data/pr_computation/ax/1ax8/1ax8.pr.out
profile	/app/data/saxs_computation/ax/1ax8/1ax8.dat