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4at5

CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH GW2580

Method: X-RAY DIFFRACTION Dmax: 64.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 543–838 Fragment：KINASE DOMAIN, RESIDUES 543-838 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

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 4AT5 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 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 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 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 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
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 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 mutation/modification 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 NTRK2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–299； UniProt 543–838

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 4at5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4at5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4at5
Deposition date deposition_date2012-05-03
Structure title titleCRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH GW2580
Keywords keywordsTRANSFERASE; TRANSFERASE
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_guinier20.74 Å
Radius of gyration Rg (electron density) rg_electron19.58 Å
Forward intensity I(0) i019737400.00
Molecular weight molecular_weight34176.0 kDa
Excluded volume excluded_volume42992 ų
Envelope volume envelope_volume50798 ų
Hydration-shell volume shell_volume21368 ų
Envelope diameter envelope_diameter65.5 Å
Shell Rg shell_rg26.20 Å
Envelope Rg envelope_rg19.90 Å
Shape Rg shape_rg19.56 Å
Total Rg total_rg20.57 Å
Total atoms total_atoms2403
Residues n_residues294
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 dmax64.3 Å
Rg (real space) rg_real20.63 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real1.9740e+07
I(0) uncertainty (real space) i0_real_error2.3740e+05
Rg (reciprocal space) rg_reciprocal20.65 Å
I(0) (reciprocal space) i0_reciprocal19740000.0000
Solution quality estimate total_estimate0.8265
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.1 Å
Skewness Skewness skewness0.168
Kurtosis Kurtosis kurtosis-0.487
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4344000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4at5a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd4at5a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id4at5A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4at5A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)