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1b8k

Neurotrophin-3 from Human

Method: X-RAY DIFFRACTION Dmax: 66.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 139–257 Not recorded No other associated polymer 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

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 1B8K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BND STRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTROPHIN 3 HETERODIMER Deposited 1994-12-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 139–257（119 aa）
Not recorded IPA ISOPROPYL ALCOHOL × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1BND STRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTROPHIN 3 HETERODIMER Deposited 1994-12-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 139–257（119 aa）
Not recorded IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1NT3 HUMAN NEUROTROPHIN-3 Deposited 1999-05-17 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 oligomeric state 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NT3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 1b8k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b8k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b8k
Deposition date deposition_date1999-02-01
Structure title titleNeurotrophin-3 from Human
Keywords keywordsCOMPLEX (GROWTH FACTOR-GROWTH FACTOR), NEUROTROPHIN, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.35 Å
Radius of gyration Rg (electron density) rg_electron17.01 Å
Forward intensity I(0) i02357410.00
Molecular weight molecular_weight10365.0 kDa
Excluded volume excluded_volume12790 ų
Envelope volume envelope_volume16096 ų
Hydration-shell volume shell_volume9160 ų
Envelope diameter envelope_diameter68.0 Å
Shell Rg shell_rg20.67 Å
Envelope Rg envelope_rg17.58 Å
Shape Rg shape_rg17.02 Å
Total Rg total_rg17.70 Å
Total atoms total_atoms726
Residues n_residues90
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax66.0 Å
Rg (real space) rg_real17.59 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real2.3570e+06
I(0) uncertainty (real space) i0_real_error3.2620e+04
Rg (reciprocal space) rg_reciprocal17.56 Å
I(0) (reciprocal space) i0_reciprocal2357000.0000
Solution quality estimate total_estimate0.7651
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.6 Å
Skewness Skewness skewness0.572
Kurtosis Kurtosis kurtosis-0.253
Angular range angular_range— – 0.4600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha338200.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.575; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.238; Smooth: 0.979
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1b8ka_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.3 — Neurotrophin

CATH v4.4 (1 domains)

Domain ID domain_id1b8kA00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
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8. Citations (2)

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9. Files and Curves (10)