SAXSdb — 5jz7

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

Beta-nerve growth factor

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 128–237 Chain B； UniProt 128–237	Not recorded	MEDI578 scFv, heavy chain × 2 MEDI578 scFv, light chain × 2	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
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain E； UniProt 128–237 Chain F； UniProt 128–237	Not recorded	MEDI578 scFv, heavy chain × 2 MEDI578 scFv, light chain × 2	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

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 5JZ7	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 oligomeric state 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 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 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 oligomeric state 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 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 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
6YW8 NMR solution structure of unbound recombinant human Nerve Growth Factor (rhNGF) Deposited 2020-04-29	Different construct 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 mutation/modification Different oligomeric state 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
9TQ6 Antibody-antigen complex Deposited 2025-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Q 169–178（10 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；291 K；50 mM imidazole, pH 7, 18% PEG 3350	Resolution 2.40 Å R-free 0.276
9TQ6 Antibody-antigen complex Deposited 2025-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 169–178（10 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；291 K；50 mM imidazole, pH 7, 18% PEG 3350	Resolution 2.40 Å R-free 0.276

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–110； UniProt 128–237 Author chain B； PDBConstruct 1–110； UniProt 128–237 Author chain E； PDBConstruct 1–110； UniProt 128–237 Author chain F； PDBConstruct 1–110； UniProt 128–237

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	5jz7
Deposition date deposition_date	2016-05-16
Structure title title	NGF IN COMPLEX WITH MEDI578 scFv
Keywords keywords	Antibody, complex, epitope, NGF, signaling protein; SIGNALING PROTEIN
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	38.78 Å
Radius of gyration Rg (electron density) rg_electron	38.82 Å
Forward intensity I(0) i0	360457000.00
Molecular weight molecular_weight	150320.0 kDa
Excluded volume excluded_volume	186360 Å³
Envelope volume envelope_volume	247040 Å³
Hydration-shell volume shell_volume	54654 Å³
Envelope diameter envelope_diameter	157.9 Å
Shell Rg shell_rg	43.06 Å
Envelope Rg envelope_rg	38.67 Å
Shape Rg shape_rg	38.78 Å
Total Rg total_rg	39.17 Å
Total atoms total_atoms	10556
Residues n_residues	1316
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	143.3 Å
Rg (real space) rg_real	39.02 Å
Rg uncertainty (real space) rg_real_error	1.54 Å
I(0) (real space) i0_real	3.6050e+08
I(0) uncertainty (real space) i0_real_error	6.7200e+06
Rg (reciprocal space) rg_reciprocal	38.87 Å
I(0) (reciprocal space) i0_reciprocal	360400000.0000
Solution quality estimate total_estimate	0.8329
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.547
Kurtosis Kurtosis kurtosis	0.079
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42910000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.664; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.910

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Beta-nerve growth factor
Molecular weight formula_weight	12421.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F
Atom count atom_count	10556

FHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKA

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 2 Entity 2 polymer

Description description	MEDI578 scFv, heavy chain
Molecular weight formula_weight	13970.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,H,J

MAQVQLVQSGAEVKKPGSSVKVSCKASGGTFSTYGISWVRQAPGQGLEWMGGIIPIFDTGNSAQSFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARSSRIYDLNPSLTAYYDMDVWGQGTMVTVSS

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

Entity 3 Entity 3 polymer

Description description	MEDI578 scFv, light chain
Molecular weight formula_weight	12695.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SAQSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAWVFGGGTKLTVLGAAAENLYFQ

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

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	5jz7A00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5jz7B00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5jz7C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5jz7D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5jz7E00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5jz7F00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5jz7G00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5jz7H00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5jz7I00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5jz7J00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5jz7K00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5jz7L00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	182.085 Å
Unit-cell length b length_b	182.085 Å
Unit-cell length c length_c	109.832 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	32

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	47.020 Å
R factor r_factor	0.2582
R_work r_work	0.2577
R_free r_free	0.2679

fit	/app/data/saxs_computation/jz/5jz7/5jz7.fit
pddf	/app/data/pr_computation/jz/5jz7/5jz7.pr.out
profile	/app/data/saxs_computation/jz/5jz7/5jz7.dat

NGF IN COMPLEX WITH MEDI578 scFv

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 (3)

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

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)