SAXSdb — 9puo

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

Leptin

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 22–167	Mutation：W100E	Neutralizing antibody Fab fragment, heavy chain × 1 Neutralizing antibody Fab fragment, light chain × 1	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 22–167	Mutation：W100E	Neutralizing antibody Fab fragment, heavy chain × 1 Neutralizing antibody Fab fragment, light chain × 1 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

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 9PUO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AX8 Human obesity protein, leptin Deposited 1997-10-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–167（146 aa）	Mutation：W100E	No recorded non-water small molecule	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
1AX8 Human obesity protein, leptin Deposited 1997-10-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–167（146 aa）	Mutation：W100E	No recorded non-water small molecule	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
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 oligomeric state 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

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

View Construct and Data Evidence

UniProt name	LEP_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–146； UniProt 22–167 Author chain F； 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	9puo
Deposition date deposition_date	2025-07-31
最后修订 last_revision	2025-11-05
Structure title title	Neutralizing monoclonal antibody Fab fragment bound to leptin
Keywords keywords	Antibody, FAB, leptin, 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	42.34 Å
Radius of gyration Rg (electron density) rg_electron	43.19 Å
Forward intensity I(0) i0	208680000.00
Molecular weight molecular_weight	115950.0 kDa
Excluded volume excluded_volume	144640 Å³
Envelope volume envelope_volume	202570 Å³
Hydration-shell volume shell_volume	43954 Å³
Envelope diameter envelope_diameter	160.0 Å
Shell Rg shell_rg	41.31 Å
Envelope Rg envelope_rg	43.77 Å
Shape Rg shape_rg	43.17 Å
Total Rg total_rg	43.15 Å
Total atoms total_atoms	16168
Residues n_residues	1084
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	152.4 Å
Rg (real space) rg_real	43.02 Å
Rg uncertainty (real space) rg_real_error	1.90 Å
I(0) (real space) i0_real	2.0870e+08
I(0) uncertainty (real space) i0_real_error	4.0070e+06
Rg (reciprocal space) rg_reciprocal	42.34 Å
I(0) (reciprocal space) i0_reciprocal	208500000.0000
Solution quality estimate total_estimate	0.7395
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.1 Å
Skewness Skewness skewness	0.746
Kurtosis Kurtosis kurtosis	0.116
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23880000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.580; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.599; Smooth: 0.270

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Neutralizing antibody Fab fragment, heavy chain
Molecular weight formula_weight	23681.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	16168

QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARSQVPSSYYYGMDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Neutralizing antibody Fab fragment, light chain
Molecular weight formula_weight	22933.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QSVLTQPPSVSGAPGQRVTISCTGGNSNIGAGYHVHWYQQLPGAAPKLLIYGDTNRPSGVPDRFSGSQSGTSASLAITGLQADDEADYYCQSYDRSRGGWFFGGGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLVSDFYPGAVTVAWKADGSPVKVGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCRVTHEGSTVEKTVAPAECS

来源 Source

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

Entity 3 Entity 3 polymer

Description description	Leptin
Molecular weight formula_weight	15984.3 kDa
Mutation mutation	W100E
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC

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	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	51.927 Å
Unit-cell length b length_b	48.534 Å
Unit-cell length c length_c	124.963 Å
Unit-cell angle α angle_alpha	90.34 °
Unit-cell angle β angle_beta	85.21 °
Unit-cell angle γ angle_gamma	70.42 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	40.170 Å
R factor r_factor	0.2403
R_work r_work	0.2363
R_free r_free	0.2772

fit	/app/data/saxs_computation/pu/9puo/9puo.fit
pddf	/app/data/pr_computation/pu/9puo/9puo.pr.out
profile	/app/data/saxs_computation/pu/9puo/9puo.dat

Neutralizing monoclonal antibody Fab fragment bound to leptin

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

Leptin

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 (4)

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 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)