SAXSdb — 1bnd

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

BRAIN DERIVED NEUROTROPHIC 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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 129–247	Not recorded	NEUROTROPHIN 3 × 2 （P20783） IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.30 Å
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 129–247	Not recorded	NEUROTROPHIN 3 × 1 （P20783） IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.30 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	BDNF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–119； UniProt 129–247

NEUROTROPHIN 3

Homo sapiens

UniProt P20783

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 139–257	Not recorded	BRAIN DERIVED NEUROTROPHIC FACTOR × 2 （P23560） IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.30 Å
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 139–257	Not recorded	BRAIN DERIVED NEUROTROPHIC FACTOR × 1 （P23560） IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.30 Å

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 1BND	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B8K Neurotrophin-3 from Human Deposited 1999-02-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 139–257（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；CRYSTALLIZATION CONDITIONS: 7% ISOPROPANOL 185 MM NACITRATE PH 5.6	Resolution 2.15 Å R-free 0.302
1NT3 HUMAN NEUROTROPHIN-3 Deposited 1999-05-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 139–257（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；200 MM AMMONIUM SULFATE, 32% PEG 400, 100 MM MES AT PH 5.6, pH 7.5	Resolution 2.40 Å R-free 0.263
3BUK Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex Deposited 2008-01-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 139–257（119 aa） Chain B 139–257（119 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；290 K；0.9M Lithium Sulfate, 0.05M Na Citrate, 0.7M Ammonium Sulfate, pH 5.0, EVAPORATION, temperature 290K	Resolution 2.60 Å R-free 0.288
9FIK Structure of the FAB fragment of the Antibody NTF30037 in complex with NTF3 Deposited 2024-05-29	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 139–257（119 aa）	Not recorded	GOL GLYCEROL × 5 PEG DI(HYDROXYETHYL)ETHER × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15 % w/v Polyethylene glycol 8,000, 0.2 M Sodium Acetate, 0.1 M MES pH 6.5	Resolution 1.86 Å R-free 0.186

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NT3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–119； UniProt 139–257

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	1bnd
Deposition date deposition_date	1994-12-12
Structure title title	STRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTROPHIN 3 HETERODIMER
Keywords keywords	NEUROTROPHIN, COMPLEX (GROWTH FACTOR-GROWTH FACTOR) COMPLEX; COMPLEX (GROWTH FACTOR/GROWTH FACTOR)
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	20.38 Å
Radius of gyration Rg (electron density) rg_electron	19.67 Å
Forward intensity I(0) i0	11794500.00
Molecular weight molecular_weight	24713.0 kDa
Excluded volume excluded_volume	30616 Å³
Envelope volume envelope_volume	37966 Å³
Hydration-shell volume shell_volume	16862 Å³
Envelope diameter envelope_diameter	68.3 Å
Shell Rg shell_rg	25.26 Å
Envelope Rg envelope_rg	20.00 Å
Shape Rg shape_rg	19.65 Å
Total Rg total_rg	20.56 Å
Total atoms total_atoms	1727
Residues n_residues	217
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	68.5 Å
Rg (real space) rg_real	20.42 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.1790e+07
I(0) uncertainty (real space) i0_real_error	1.6710e+05
Rg (reciprocal space) rg_reciprocal	20.41 Å
I(0) (reciprocal space) i0_reciprocal	11790000.0000
Solution quality estimate total_estimate	0.8051
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.388
Kurtosis Kurtosis kurtosis	-0.341
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1523000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.000

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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	BRAIN DERIVED NEUROTROPHIC FACTOR
Molecular weight formula_weight	13534.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1937

HSDPARRGQLSVCDSISEWVTAADKKTAVDMSGGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRALTMDSKKRIGWRFIRIDTSCVCTLTIKRGR

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	NEUROTROPHIN 3
Molecular weight formula_weight	13656.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

YAEHKSHRGEVSVCDSESLWVTDKSSAIDIRGHQVTVLGEIKTQNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRIDTSCVCALSRKIGRT

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 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bnda_
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	d1bndb_
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	1bndA00
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	1bndB00
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 (2)

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Unit-cell length a length_a	98.400 Å
Unit-cell length b length_b	45.100 Å
Unit-cell length c length_c	68.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	—

fit	/app/data/saxs_computation/bn/1bnd/1bnd.fit
pddf	/app/data/pr_computation/bn/1bnd/1bnd.pr.out
profile	/app/data/saxs_computation/bn/1bnd/1bnd.dat

STRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTROPHIN 3 HETERODIMER

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

BRAIN DERIVED NEUROTROPHIC FACTOR

State in the Current Structure

Other States of the Same Protein in the Database

NEUROTROPHIN 3

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

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 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)