SAXSdb — 1hcf

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

NEUROTROPHIN-4

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 81–210 Chain B； UniProt 81–210	Fragment：ACTIVE, FRAGMENT. PRO-REGION CLEAVED	BDNF/NT-3 GROWTH FACTORS RECEPTOR × 2 （Q16620） 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

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 1HCF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B98 NEUROTROPHIN 4 (HOMODIMER) Deposited 1999-02-22	Different construct 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 81–210（130 aa） Fragment：precursor residues 81-210 Chain M 81–210（130 aa） Fragment：precursor residues 81-210	Not recorded	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

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 B； PDBConstruct 1–130； UniProt 81–210

BDNF/NT-3 GROWTH FACTORS RECEPTOR

HOMO SAPIENS

UniProt Q16620

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 X； UniProt 286–383 Chain Y； UniProt 286–383	Fragment：EXTRACELLULAR DOMAIN 5 (RESIDUES 286 - 383)	NEUROTROPHIN-4 × 2 （P34130） 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

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 1HCF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WWB LIGAND BINDING DOMAIN OF HUMAN TRKB RECEPTOR Deposited 1999-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 283–385（103 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.10 Å R-free 0.297
2MFQ NMR solution structures of FRS2a PTB domain with neurotrophin receptor TrkB Deposited 2013-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 497–519（23 aa） Fragment：UNP residues 497-519	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 100 mM sodium phosphate, 5 mM [U-100% 2H] DTT, 0.5 mM [U-100% 2H] EDTA, 100% D2O \| 100% D2O NMR sample composition 100 mM sodium phosphate, 5 mM [U-100% 2H] DTT, 0.5 mM [U-100% 2H] EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4ASZ Crystal structure of apo TrkB kinase domain Deposited 2012-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 543–838（296 aa） Fragment：KINASE DOMAIN, RESIDUES 543-838	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；277 K；THE APO-TRKB PROTEIN WAS CONCENTRATED TO 6 MG/ML AND CRYSTALLIZED IN 3 M NA-FORMATE, PH 8.0 AT 4 DEGREES C.	Resolution 1.70 Å R-free 0.203
4AT3 CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH CPD5N Deposited 2012-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 543–838（296 aa） Fragment：KINASE DOMAIN, RESIDUES 543-838	Not recorded	LTI (5Z)-5-(carbamoylimino)-3-[(5R)-6,7,8,9-tetrahydro-5H-benzo[7]annulen-5-ylsulfanyl]-2,5-dihydroisothiazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；277 K；THE TRKB-CPD5N COMPLEX WAS OBTAINED BY COCRYSTALLIZATION IN 1.6 M AMMONIUM SULFATE, 50 MM MES, PH 6.0 AT 4 DEGREESC IN PRESENCE OF 2 MM OF INHIBITOR.	Resolution 1.77 Å R-free 0.224
4AT4 CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH EX429 Deposited 2012-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 543–838（296 aa） Fragment：KINASE DOMAIN, RESIDUES 543-838	Not recorded	T6E 1-[4-(4-aminothieno[2,3-d]pyrimidin-5-yl)phenyl]-3-[2-fluoro-5-(trifluoromethyl)phenyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；277 K；THE TRKB-EX429 COMPLEX WAS OBTAINED BY COCRYSTALLIZATION IN 2.1 M NA-FORMATE, 50 MM HEPES, PH 8.0 AT 4 DEGREES C IN PRESENCE OF 1 MM OF INHIBITOR.	Resolution 2.36 Å R-free 0.217
4AT5 CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH GW2580 Deposited 2012-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 543–838（296 aa） Fragment：KINASE DOMAIN, RESIDUES 543-838	Not recorded	MUJ 5-{3-methoxy-4-[(4-methoxybenzyl)oxy]benzyl}pyrimidine-2,4-diamine × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；277 K；THE TRKB-GW2580 COMPLEX WAS OBTAINED BY COCRYSTALLIZATION IN 2.4 M NA-FORMATE, 50 MM HEPES, PH 8.0 AT 4 DEGREES C IN PRESENCE OF 2 MM OF INHIBITOR.	Resolution 1.71 Å R-free 0.186
5MO9 Structure of human TrkB receptor ligand binding domain in complex with the Fab frgment of antibody AB20 Deposited 2016-12-14	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 X 278–426（149 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；6% w/v PEG 3350, 25 mM Tris pH 8.5	Resolution 2.59 Å R-free 0.224
8OYD TrkB transmembrane domain NMR structure in DMPC/DHPC bicelles Deposited 2023-05-04	Different construct Different oligomeric state 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 422–466（45 aa） Chain B 422–466（45 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 20；Pressure AMBIENT NMR sample composition 5 % v/v [U-2H] D2O, 1.1 mM [U-100% 13C; U-100% 15N] High affinity receptor of neurotrophin-4 and brain-derived neurotrophic factor (TrkB), 9.6 mM [U-2H] DMPC, 42.7 mM [U-2H] DHPC, 1.0 mM n.a. TCEP, 0.01 % w/v n.a. sodium azide, 20.0 mM n.a. sodium phosphate buffer, 0.5 mM d4 TSP, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRKB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain X； PDBConstruct 4–101； UniProt 286–383 Author chain Y； PDBConstruct 4–101； UniProt 286–383

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	1hcf
Deposition date deposition_date	2001-05-03
Structure title title	Crystal structure of TrkB-d5 bound to neurotrophin-4/5
Keywords keywords	;TRANSFERASE/HORMONE, COMPLEX(TRANSFERASE-GROWTH FACTOR), NEUROTROPHIN-4/5, TRKB RECEPTOR, NGF-BETA SUPERFAMILY, IMMUNOGLOBULIN DOMAIN, TRANSFERASE-HORMONE complex ;; TRANSFERASE/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	25.95 Å
Radius of gyration Rg (electron density) rg_electron	25.69 Å
Forward intensity I(0) i0	44467200.00
Molecular weight molecular_weight	49001.0 kDa
Excluded volume excluded_volume	60131 Å³
Envelope volume envelope_volume	75328 Å³
Hydration-shell volume shell_volume	25900 Å³
Envelope diameter envelope_diameter	97.9 Å
Shell Rg shell_rg	31.12 Å
Envelope Rg envelope_rg	25.77 Å
Shape Rg shape_rg	25.72 Å
Total Rg total_rg	26.18 Å
Total atoms total_atoms	3439
Residues n_residues	444
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	94.4 Å
Rg (real space) rg_real	26.06 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	4.4470e+07
I(0) uncertainty (real space) i0_real_error	7.0140e+05
Rg (reciprocal space) rg_reciprocal	26.03 Å
I(0) (reciprocal space) i0_reciprocal	44470000.0000
Solution quality estimate total_estimate	0.8387
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.520
Kurtosis Kurtosis kurtosis	0.046
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9798000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.683; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.992

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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	NEUROTROPHIN-4
Molecular weight formula_weight	13944.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3499

GVSETAPASRRGELAVCDAVSGWVTDRRTAVDLRGREVEVLGEVPAAGGSPLRQYFFETRCKADNAEEGGPGAGGGGCRGVDRRHWVSECKAKQSYVRALTADAQGRVGWRWIRIDTACVCTLLSRTGRA

Entity 2 Entity 2 polymer

Description description	BDNF/NT-3 GROWTH FACTORS RECEPTOR
Molecular weight formula_weight	11546.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y

SHMAPTITFLESPTSDHHWCIPFTVKGNPKPALQWFYNGAILNESKYICTKIHVTNHTEYHGCLQLDNPTHMNNGDYTLIAKNEYGKDEKQISAHFMGWPG

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

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

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1hcfa_
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	d1hcfb_
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	d1hcfx_
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.1.1.4 — I set domains

Domain ID domain_id	d1hcfy_
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.1.1.4 — I set domains

CATH v4.4 (4 domains)

Domain ID domain_id	1hcfA00
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	1hcfB00
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	1hcfX00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1hcfY00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (5)

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Unit-cell length a length_a	74.372 Å
Unit-cell length b length_b	80.406 Å
Unit-cell length c length_c	91.318 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2640

fit	/app/data/saxs_computation/hc/1hcf/1hcf.fit
pddf	/app/data/pr_computation/hc/1hcf/1hcf.pr.out
profile	/app/data/saxs_computation/hc/1hcf/1hcf.dat

Crystal structure of TrkB-d5 bound to neurotrophin-4/5

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

NEUROTROPHIN-4

State in the Current Structure

Other States of the Same Protein in the Database

BDNF/NT-3 GROWTH FACTORS RECEPTOR

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

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (5)

9. Files and Curves (10)

Files (7)

Curves (3)