4edx

Nerve Growth Factor in Complex with Fab from mouse mAb 911

Method: X-RAY DIFFRACTION D_max: 159.7 Å Quality: REASONABLE

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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 V； UniProt 122–241 Chain W； UniProt 122–241	Not recorded	light chain of FAB of murine anti-NGF × 2 heavy chain of Fab of murine anti-NGF × 2	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

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 4EDX	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 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 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 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
4ZBN Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor Deposited 2015-04-15	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 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 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 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 11 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 V； PDBConstruct 1–120； UniProt 122–241 Author chain W； PDBConstruct 1–120； UniProt 122–241

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4edx
Deposition date deposition_date	2012-03-27
Structure title title	Nerve Growth Factor in Complex with Fab from mouse mAb 911
Keywords keywords	cystine knot, immunoglobulin, growth/survival factor, 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	43.76 Å
Radius of gyration Rg (electron density) rg_electron	44.53 Å
Forward intensity I(0) i0	214018000.00
Molecular weight molecular_weight	116670.0 kDa
Excluded volume excluded_volume	144950 Å³
Envelope volume envelope_volume	202320 Å³
Hydration-shell volume shell_volume	42934 Å³
Envelope diameter envelope_diameter	166.3 Å
Shell Rg shell_rg	41.83 Å
Envelope Rg envelope_rg	44.99 Å
Shape Rg shape_rg	44.49 Å
Total Rg total_rg	44.51 Å
Total atoms total_atoms	8200
Residues n_residues	1047
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	159.7 Å
Rg (real space) rg_real	44.59 Å
Rg uncertainty (real space) rg_real_error	2.12 Å
I(0) (real space) i0_real	2.1400e+08
I(0) uncertainty (real space) i0_real_error	4.3760e+06
Rg (reciprocal space) rg_reciprocal	43.77 Å
I(0) (reciprocal space) i0_reciprocal	213800000.0000
Solution quality estimate total_estimate	0.7125
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.5 Å
Skewness Skewness skewness	0.728
Kurtosis Kurtosis kurtosis	-0.063
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22600000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.463; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.339; Smooth: 0.532

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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	Beta-nerve growth factor
Molecular weight formula_weight	13515.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W,V
Atom count atom_count	8298

SSSHPIFHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKAVRRA

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 2 Entity 2 polymer

Description description	light chain of FAB of murine anti-NGF
Molecular weight formula_weight	23779.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DIQMTQTTSSLSASLGDRVTISCRASQDISNHLNWYQQKPDGTVKLLIYYISRFHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQSKTLPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	heavy chain of Fab of murine anti-NGF
Molecular weight formula_weight	23681.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QVQLKESGPGLVAPSQSLSITCTVSGFSLIGYDINWVRQPPGKGLEWLGMIWGDGTTDYNSALKSRLSISKDNSKSQVFLKMNSLRTDDTATYSCARGGYYYGTSYYFDYWGQGTTLTVSSASTTPPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4edxa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4edxa2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d4edxb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4edxh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4edxl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4edxl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d4edxv_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.3 — Neurotrophin

Domain ID domain_id	d4edxw_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.3 — Neurotrophin

CATH v4.4 (10 domains)

Domain ID domain_id	4edxA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4edxA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4edxB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4edxB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4edxH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4edxH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4edxL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4edxL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4edxV00
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	4edxW00
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

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8. Citations (1)

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Unit-cell length a length_a	57.748 Å
Unit-cell length b length_b	69.931 Å
Unit-cell length c length_c	83.736 Å
Unit-cell angle α angle_alpha	104.34 °
Unit-cell angle β angle_beta	94.13 °
Unit-cell angle γ angle_gamma	110.42 °
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	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.490 Å
R factor r_factor	0.2093
R_work r_work	0.2080
R_free r_free	0.2579

fit	/app/data/saxs_computation/ed/4edx/4edx.fit
pddf	/app/data/pr_computation/ed/4edx/4edx.pr.out
profile	/app/data/saxs_computation/ed/4edx/4edx.dat

Nerve Growth Factor in Complex with Fab from mouse mAb 911

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

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 water

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)