SAXSdb — 4xpj

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 122–241 Chain B； UniProt 122–241	Not recorded	LPY (2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1 M imidazole, 1.0 M Na acetate	Resolution 2.60 Å R-free 0.266

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 4XPJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BET NEW PROTEIN FOLD REVEALED BY A 2.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF NERVE GROWTH FACTOR Deposited 1993-04-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 131–237（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1BTG CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND Deposited 1995-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 130–239（110 aa） Chain B 130–239（110 aa） Chain C 130–239（110 aa）	Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED)	ZN ZINC ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1BTG CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND Deposited 1995-08-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 130–239（110 aa）	Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1BTG CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND Deposited 1995-08-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 130–239（110 aa） Chain C 130–239（110 aa）	Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED)	ZN ZINC ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1BTG CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND Deposited 1995-08-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 130–239（110 aa） Chain C 130–239（110 aa）	Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) Mutation：BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED)	ZN ZINC ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1SGF CRYSTAL STRUCTURE OF 7S NGF: A COMPLEX OF NERVE GROWTH FACTOR WITH FOUR BINDING PROTEINS (SERINE PROTEINASES) Deposited 1997-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 122–239（118 aa） Chain Y 122–239（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.9；PROTEIN WAS CRYSTALLIZED FROM 20MG/ML PROTEIN SOLUTION IN 50MM SODIUM PHOSPHATE (PH6.8) MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION (50MM SODIUM ACETATE PH4.5-5.1, 12-21% PEG 4000, 10 MICROMOLAR ZNSO4) (MCDONALD AND BLUNDELL, 1991, JMB, 219, 595-601)., pH 4.9	Resolution 3.15 Å R-free 0.282
3IJ2 Ligand-receptor structure Deposited 2009-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 129–351（223 aa） Fragment：UNP RESIDUES 129-241 Chain B 129–351（223 aa） Fragment：UNP RESIDUES 129-241	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.75 Å R-free 0.274
4EAX Mouse NGF in complex with Lyso-PS Deposited 2012-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 122–241（120 aa） Chain B 122–241（120 aa）	Not recorded	S12 O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M Imidazole, 1.0M Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.259
4EAX Mouse NGF in complex with Lyso-PS Deposited 2012-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 122–241（120 aa） Chain D 122–241（120 aa）	Not recorded	S12 O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M Imidazole, 1.0M Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.259
5LSD Recombinant mouse Nerve Growth Factor Deposited 2016-08-25	Different construct Different ligand/ion 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 measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM sodium phosphate, 1 mM EDTA, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
6FFY Structure of the mouse SorCS2-NGF complex Deposited 2018-01-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 122–238（117 aa） Chain C 122–238（117 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；291 K；0.225 M MES/bis-tris pH 6.6 and 6.6 % w/v PEG 6000	Resolution 3.90 Å R-free 0.305

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NGF_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–120； UniProt 122–241 Author chain B； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4xpj
Deposition date deposition_date	2015-01-17
Structure title title	Crystal structure of Nerve growth factor in complex with lysophosphatidylinositol
Keywords keywords	Nerve Growth Factor, LysoPI, HORMONE; HORMONE
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	20.78 Å
Radius of gyration Rg (electron density) rg_electron	19.84 Å
Forward intensity I(0) i0	11075500.00
Molecular weight molecular_weight	24125.0 kDa
Excluded volume excluded_volume	29949 Å³
Envelope volume envelope_volume	37209 Å³
Hydration-shell volume shell_volume	16544 Å³
Envelope diameter envelope_diameter	72.2 Å
Shell Rg shell_rg	25.37 Å
Envelope Rg envelope_rg	20.22 Å
Shape Rg shape_rg	19.84 Å
Total Rg total_rg	20.68 Å
Total atoms total_atoms	1690
Residues n_residues	210
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	72.2 Å
Rg (real space) rg_real	20.85 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.1080e+07
I(0) uncertainty (real space) i0_real_error	1.4360e+05
Rg (reciprocal space) rg_reciprocal	20.83 Å
I(0) (reciprocal space) i0_reciprocal	11080000.0000
Solution quality estimate total_estimate	0.8713
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.419
Kurtosis Kurtosis kurtosis	-0.275
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1245000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4xpja_
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	d4xpjb_
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 (2 domains)

Domain ID domain_id	4xpjA00
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	4xpjB00
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	96.689 Å
Unit-cell length b length_b	96.689 Å
Unit-cell length c length_c	164.339 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	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.605 Å
Low-resolution limit resolution_low	37.304 Å
R factor r_factor	0.1987
R_work r_work	0.1952
R_free r_free	0.2658

Description description	Beta-nerve growth factor
Molecular weight formula_weight	13491.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1750

Crystal structure of Nerve growth factor in complex with lysophosphatidylinositol

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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	(2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate
Molecular weight formula_weight	530.5 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

fit	/app/data/saxs_computation/xp/4xpj/4xpj.fit
pddf	/app/data/pr_computation/xp/4xpj/4xpj.pr.out
profile	/app/data/saxs_computation/xp/4xpj/4xpj.dat