SAXSdb — 1b98

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

PROTEIN (NEUROTROPHIN-4)

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 81–210 Chain M； UniProt 81–210	Fragment：precursor residues 81-210	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；PEG 8000, PIPES, pH 6.50	Resolution 2.75 Å R-free 0.336

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 1B98	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HCF Crystal structure of TrkB-d5 bound to neurotrophin-4/5 Deposited 2001-05-03	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 81–210（130 aa） Fragment：ACTIVE, FRAGMENT. PRO-REGION CLEAVED Chain B 81–210（130 aa） Fragment：ACTIVE, FRAGMENT. PRO-REGION CLEAVED	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10 MG/ML COMPLEX IN 20MM TRIS, 150MM NACL, PH 7.5, 100MM HEPES PH 7.5, 1.5M LISO4	Resolution 2.70 Å R-free 0.264

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NT5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–130； UniProt 81–210 Author chain M； PDBConstruct 1–130； UniProt 81–210

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	1b98
Deposition date deposition_date	1999-02-22
Structure title title	NEUROTROPHIN 4 (HOMODIMER)
Keywords keywords	TARGET-DERIVED SURVIVAL FACTOR, NEUROTROPHIN 4, NEUROTROPHIN 5, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/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	19.76 Å
Radius of gyration Rg (electron density) rg_electron	18.82 Å
Forward intensity I(0) i0	11118800.00
Molecular weight molecular_weight	23159.0 kDa
Excluded volume excluded_volume	28332 Å³
Envelope volume envelope_volume	35199 Å³
Hydration-shell volume shell_volume	16187 Å³
Envelope diameter envelope_diameter	66.2 Å
Shell Rg shell_rg	24.35 Å
Envelope Rg envelope_rg	19.24 Å
Shape Rg shape_rg	18.85 Å
Total Rg total_rg	19.58 Å
Total atoms total_atoms	1622
Residues n_residues	216
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	65.8 Å
Rg (real space) rg_real	19.77 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	1.1120e+07
I(0) uncertainty (real space) i0_real_error	1.3780e+05
Rg (reciprocal space) rg_reciprocal	19.77 Å
I(0) (reciprocal space) i0_reciprocal	11120000.0000
Solution quality estimate total_estimate	0.8902
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.331
Kurtosis Kurtosis kurtosis	-0.399
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1532000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.994

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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	PROTEIN (NEUROTROPHIN-4)
Molecular weight formula_weight	13944.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,M
Atom count atom_count	1671

GVSETAPASRRGELAVCDAVSGWVTDRRTAVDLRGREVEVLGEVPAAGGSPLRQYFFETRCKADNAEEGGPGAGGGGCRGVDRRHWVSECKAKQSYVRALTADAQGRVGWRWIRIDTACVCTLLSRTGRA

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 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b98a_
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	d1b98m_
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	1b98A00
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	1b98M00
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 (3)

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Unit-cell length a length_a	43.800 Å
Unit-cell length b length_b	50.800 Å
Unit-cell length c length_c	53.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.3360

fit	/app/data/saxs_computation/b9/1b98/1b98.fit
pddf	/app/data/pr_computation/b9/1b98/1b98.pr.out
profile	/app/data/saxs_computation/b9/1b98/1b98.dat

NEUROTROPHIN 4 (HOMODIMER)

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

PROTEIN (NEUROTROPHIN-4)

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