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6fdy

Unc-51-Like Kinase 3 (ULK3) In Complex With Bosutinib

Method: X-RAY DIFFRACTION Dmax: 63.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase ULK3

Homo sapiens

UniProt Q6PHR2

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 U； UniProt 2–277 Not recorded DB8 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris pH 8.5; 0.2 M sodium citrate; 30% PEG400 Resolution 1.70 Å R-free 0.239

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 6FDY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4WZX ULK3 regulates cytokinetic abscission by phosphorylating ESCRT-III proteins Deposited 2014-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 359–449（91 aa） Fragment：MIT 2 domain (UNP residues 359-449)
Not recorded CO COBALT (II) ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；50mM MES pH 6.5, 5mM Cobalt chloride, 800mM ammonium sulfate
Resolution 1.39 Å R-free 0.180
6FDZ Unc-51-Like Kinase 3 (ULK3) In Complex With Momelotinib Deposited 2017-12-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain U 2–277（276 aa）
Not recorded C87 Momelotinib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 0.2 M MgCl2, 30% 2-propanol
Resolution 2.55 Å R-free 0.301

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ULK3_HUMAN
Isoform Q6PHR2-3
PDB entities 1
Chains and sequence ranges Author chain U； PDBConstruct 1–276； UniProt 2–277

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 6fdy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6fdy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6fdy
Deposition date deposition_date2017-12-27
Structure title titleUnc-51-Like Kinase 3 (ULK3) In Complex With Bosutinib
Keywords keywordsKinase Inhibitor DFG-in, transferase; 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_guinier20.25 Å
Radius of gyration Rg (electron density) rg_electron19.14 Å
Forward intensity I(0) i015187200.00
Molecular weight molecular_weight30153.0 kDa
Excluded volume excluded_volume38067 ų
Envelope volume envelope_volume45274 ų
Hydration-shell volume shell_volume19829 ų
Envelope diameter envelope_diameter65.7 Å
Shell Rg shell_rg25.46 Å
Envelope Rg envelope_rg19.30 Å
Shape Rg shape_rg19.11 Å
Total Rg total_rg20.19 Å
Total atoms total_atoms2119
Residues n_residues261
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 dmax63.3 Å
Rg (real space) rg_real20.16 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real1.5190e+07
I(0) uncertainty (real space) i0_real_error1.8650e+05
Rg (reciprocal space) rg_reciprocal20.18 Å
I(0) (reciprocal space) i0_reciprocal15190000.0000
Solution quality estimate total_estimate0.7322
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.3 Å
Skewness Skewness skewness0.204
Kurtosis Kurtosis kurtosis-0.416
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3652000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 0.260; Positv: 1.000; Valcen: 0.994; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6fdyu_
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

CATH v4.4 (2 domains)

Domain ID domain_id6fdyU01
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_id6fdyU02
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)