SAXSdb — 9tq6

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

Beta-nerve growth factor

OrganismNot specified

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 Q； UniProt 169–178	Non-standard monomer：Yes (specific site not provided by mmCIF)	Antibody Fab fragment heavy chain × 1 Antibody Fab fragment light chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；50 mM imidazole, pH 7, 18% PEG 3350	Resolution 2.40 Å R-free 0.276
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain P； UniProt 169–178	Non-standard monomer：Yes (specific site not provided by mmCIF)	Antibody Fab fragment heavy chain × 1 Antibody Fab fragment light chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；50 mM imidazole, pH 7, 18% PEG 3350	Resolution 2.40 Å R-free 0.276

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 9TQ6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SG1 Crystal Structure of the Receptor-Ligand Complex between Nerve Growth Factor and the Common Neurotrophin Receptor p75 Deposited 2004-02-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 122–241（120 aa） Chain B 122–241（120 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；295 K；PEG 1000, isoproponal, sodium chloride, citrate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.269
1WWW NGF IN COMPLEX WITH DOMAIN 5 OF THE TRKA RECEPTOR Deposited 1999-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 122–241（120 aa） Chain W 122–241（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 2.20 Å R-free 0.266
2IFG Structure of the extracellular segment of human TRKA in complex with nerve growth factor Deposited 2006-09-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 122–241（120 aa） Chain F 122–241（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PEG, GLYCINE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 7.50	Resolution 3.40 Å R-free 0.331
4EDW Nerve Growth Factor in Complex with Fab from humanized version of mouse mAb 911 (tanezumab) Deposited 2012-03-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 122–241（120 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；300 K；PEG 5000 monomethylether, glycerol, sodium cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.48 Å R-free 0.249
4EDX Nerve Growth Factor in Complex with Fab from mouse mAb 911 Deposited 2012-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain V 122–241（120 aa） Chain W 122–241（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；300 K；PEG 3350, zinc acetate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.50 Å R-free 0.258
4ZBN Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor Deposited 2015-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 122–241（120 aa） Chain B 122–241（120 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；16 % PEG 8000, 100 mM HEPES pH 6.0, 100 mM Magnesium Acetate and 20% glycerol	Resolution 2.45 Å R-free 0.257
5JZ7 NGF IN COMPLEX WITH MEDI578 scFv Deposited 2016-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 128–237（110 aa） Chain B 128–237（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；18 % PEG 8000, 150 mM NaCl, 100 mM MES pH 6.5	Resolution 3.40 Å R-free 0.268
5JZ7 NGF IN COMPLEX WITH MEDI578 scFv Deposited 2016-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 128–237（110 aa） Chain F 128–237（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；18 % PEG 8000, 150 mM NaCl, 100 mM MES pH 6.5	Resolution 3.40 Å R-free 0.268
6YW8 NMR solution structure of unbound recombinant human Nerve Growth Factor (rhNGF) Deposited 2020-04-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 122–239（118 aa） Chain B 122–239（118 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.1 mM [U-99% 15N] Nerve Growth Factor, 50 mM HEPES, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM HEPES, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9TPP Antibody-antigen complex Deposited 2025-12-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 169–179（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；0.1M HEPES, pH 7.5, 18% PEG 3350, 20% isopropanol	Resolution 1.80 Å R-free 0.202

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NGF_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 2–11； UniProt 169–178 Author chain Q； PDBConstruct 2–11； UniProt 169–178

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	9tq6
Deposition date deposition_date	2025-12-19
最后修订 last_revision	2026-05-27
Structure title title	Antibody-antigen complex
Keywords keywords	antibody, nitrotyrosine, complex, PROTEIN BINDING; PROTEIN BINDING
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	33.63 Å
Radius of gyration Rg (electron density) rg_electron	32.84 Å
Forward intensity I(0) i0	145307000.00
Molecular weight molecular_weight	95353.0 kDa
Excluded volume excluded_volume	118940 Å³
Envelope volume envelope_volume	161210 Å³
Hydration-shell volume shell_volume	41368 Å³
Envelope diameter envelope_diameter	108.6 Å
Shell Rg shell_rg	39.40 Å
Envelope Rg envelope_rg	32.03 Å
Shape Rg shape_rg	32.83 Å
Total Rg total_rg	33.45 Å
Total atoms total_atoms	6719
Residues n_residues	866
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	108.5 Å
Rg (real space) rg_real	33.56 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	1.4530e+08
I(0) uncertainty (real space) i0_real_error	2.6110e+06
Rg (reciprocal space) rg_reciprocal	33.61 Å
I(0) (reciprocal space) i0_reciprocal	145300000.0000
Solution quality estimate total_estimate	0.8993
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.9 Å
Skewness Skewness skewness	0.215
Kurtosis Kurtosis kurtosis	-0.460
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13540000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.912

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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	Antibody Fab fragment heavy chain
Molecular weight formula_weight	25826.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,H
Atom count atom_count	6765

MKCSWVIFFLMAVVTGVNSEVQLQQSGAELVKPGASVKLSCTASDFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATISADTSSNTAYLHLSSLTSEDTAVYYCASLWSYWYFDVWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Entity 2 Entity 2 polymer

Description description	Antibody Fab fragment light chain
Molecular weight formula_weight	26438.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MDSQAQVLILLLLWVSGTCGDIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQFYNLFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 3 Entity 3 polymer

Description description	Beta-nerve growth factor
Molecular weight formula_weight	1409.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

XVFKQYFFETK

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	46

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8. Citations (1)

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Unit-cell length a length_a	71.555 Å
Unit-cell length b length_b	91.277 Å
Unit-cell length c length_c	142.411 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	45.640 Å
R factor r_factor	0.2373
R_work r_work	0.2352
R_free r_free	0.2759

fit	/app/data/saxs_computation/tq/9tq6/9tq6.fit
pddf	/app/data/pr_computation/tq/9tq6/9tq6.pr.out
profile	/app/data/saxs_computation/tq/9tq6/9tq6.dat

Antibody-antigen complex

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

Beta-nerve growth factor

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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)