SAXSdb — 5mo9

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

BDNF/NT-3 growth factors receptor

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain X； UniProt 278–426	Not recorded	AB20 Fab heavy chain × 1 AB20 Fab light chain × 1	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

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 5MO9	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
1WWB LIGAND BINDING DOMAIN OF HUMAN TRKB RECEPTOR Deposited 1999-05-03	Different construct Different oligomeric state 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 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 oligomeric state 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 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 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 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
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	3
Chains and sequence ranges	Author chain X； PDBConstruct 3–151； UniProt 278–426

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	5mo9
Deposition date deposition_date	2016-12-14
Structure title title	Structure of human TrkB receptor ligand binding domain in complex with the Fab frgment of antibody AB20
Keywords keywords	Trk receptor, antibody, antigen, complex, immune system; IMMUNE SYSTEM
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	28.65 Å
Radius of gyration Rg (electron density) rg_electron	28.10 Å
Forward intensity I(0) i0	55266400.00
Molecular weight molecular_weight	58036.0 kDa
Excluded volume excluded_volume	72481 Å³
Envelope volume envelope_volume	93025 Å³
Hydration-shell volume shell_volume	28932 Å³
Envelope diameter envelope_diameter	102.7 Å
Shell Rg shell_rg	33.94 Å
Envelope Rg envelope_rg	28.00 Å
Shape Rg shape_rg	28.08 Å
Total Rg total_rg	28.74 Å
Total atoms total_atoms	4091
Residues n_residues	533
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	96.5 Å
Rg (real space) rg_real	28.77 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	5.5270e+07
I(0) uncertainty (real space) i0_real_error	9.0310e+05
Rg (reciprocal space) rg_reciprocal	28.72 Å
I(0) (reciprocal space) i0_reciprocal	55260000.0000
Solution quality estimate total_estimate	0.8690
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.6 Å
Skewness Skewness skewness	0.488
Kurtosis Kurtosis kurtosis	-0.196
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8084000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.886; Smooth: 0.873

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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	AB20 Fab heavy chain
Molecular weight formula_weight	23675.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	4337

QVQLQQSGAELVRPGASVTLSCKASGYTFTDYEMHWVKQTPVHGLEWIGTIDPETAGTAYNQKFKGKAILTAGKSSSTAYMELRSLTSEDSAVYYCTGVTTWFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	AB20 Fab light chain
Molecular weight formula_weight	23931.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPNLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	BDNF/NT-3 growth factors receptor
Molecular weight formula_weight	16909.6 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MGSVNLTVHFAPTITFLESPTSDHHWCIPFTVKGNPKPALQWFYNGAILNESKYICTKIHVTNHTEYHGCLQLDNPTHMNNGDYTLIAKNEYGKDEKQISAHFMGWPGIDDGANPNYPDVIYEDYGTAANDIGDTTNRSNEIPSTDVTDKT

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 BL21(DE3)

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5mo9h1
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.1.1.0 — automated matches

Domain ID domain_id	d5mo9h2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5mo9l1
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.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5mo9l2
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.1.1.0 — automated matches

Domain ID domain_id	d5mo9x_
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.1.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	5mo9H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5mo9H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5mo9L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5mo9L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5mo9X00
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	148.370 Å
Unit-cell length b length_b	55.430 Å
Unit-cell length c length_c	69.390 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.594 Å
Low-resolution limit resolution_low	37.000 Å
R factor r_factor	0.1820
R_work r_work	0.1900
R_free r_free	0.2240

fit	/app/data/saxs_computation/mo/5mo9/5mo9.fit
pddf	/app/data/pr_computation/mo/5mo9/5mo9.pr.out
profile	/app/data/saxs_computation/mo/5mo9/5mo9.dat

Structure of human TrkB receptor ligand binding domain in complex with the Fab frgment of antibody AB20

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

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)