SAXSdb — 1wwb

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

PROTEIN (Brain Derived Neurotrophic Factor Receptor TrkB)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain X； UniProt 283–385	Fragment：LIGAND BINDING DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.5	Resolution 2.10 Å R-free 0.297

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 1WWB	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 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 X 286–383（98 aa） Fragment：EXTRACELLULAR DOMAIN 5 (RESIDUES 286 - 383) Chain Y 286–383（98 aa） Fragment：EXTRACELLULAR DOMAIN 5 (RESIDUES 286 - 383)	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
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 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 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 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 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 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 oligomeric state 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 mutation/modification Different oligomeric state 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	NTRK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–103； UniProt 283–385

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	1wwb
Deposition date deposition_date	1999-05-03
Structure title title	LIGAND BINDING DOMAIN OF HUMAN TRKB RECEPTOR
Keywords keywords	TRK RECEPTOR, RECEPTOR TYROSINE KINASE, 3D-DOMAIN SWAPPING, TRANSFERASE; TRANSFERASE
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	19.32 Å
Radius of gyration Rg (electron density) rg_electron	19.54 Å
Forward intensity I(0) i0	2865630.00
Molecular weight molecular_weight	11767.0 kDa
Excluded volume excluded_volume	14671 Å³
Envelope volume envelope_volume	21173 Å³
Hydration-shell volume shell_volume	10645 Å³
Envelope diameter envelope_diameter	70.4 Å
Shell Rg shell_rg	22.86 Å
Envelope Rg envelope_rg	21.86 Å
Shape Rg shape_rg	19.57 Å
Total Rg total_rg	20.13 Å
Total atoms total_atoms	832
Residues n_residues	103
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	70.5 Å
Rg (real space) rg_real	19.78 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	2.8660e+06
I(0) uncertainty (real space) i0_real_error	4.4900e+04
Rg (reciprocal space) rg_reciprocal	19.71 Å
I(0) (reciprocal space) i0_reciprocal	2866000.0000
Solution quality estimate total_estimate	0.7356
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.9 Å
Skewness Skewness skewness	0.773
Kurtosis Kurtosis kurtosis	0.047
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	313000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.442; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.297; Smooth: 0.937

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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_id	d1wwbx_
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 (1 domains)

Domain ID domain_id	1wwbX00
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 (1)

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Unit-cell length a length_a	68.340 Å
Unit-cell length b length_b	68.340 Å
Unit-cell length c length_c	124.340 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	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2470
R_free r_free	0.2970

Description description	PROTEIN (Brain Derived Neurotrophic Factor Receptor TrkB)
Molecular weight formula_weight	11802.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	906

LIGAND BINDING DOMAIN OF HUMAN TRKB RECEPTOR

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

PROTEIN (Brain Derived Neurotrophic Factor Receptor TrkB)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	74

fit	/app/data/saxs_computation/ww/1wwb/1wwb.fit
pddf	/app/data/pr_computation/ww/1wwb/1wwb.pr.out
profile	/app/data/saxs_computation/ww/1wwb/1wwb.dat