8s9f

Crystal structure of the kinase domain of Bruton's Tyrosine Kinase bound to dasatinib

Method: X-RAY DIFFRACTION Dmax: 90.2 Å Quality: EXCELLENT

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

Tyrosine-protein kinase BTK

Mus musculus

UniProt P35991

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 382–659 Chain B; UniProt 382–659 Mutation:L390G, Y551E, Y617P 1N1 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;42% PEG200, 0.1M HEPES Resolution 2.60 Å R-free 0.284

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.

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BTK_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–279; UniProt 382–659 Author chain B; PDBConstruct 2–279; UniProt 382–659

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 8s9f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8s9f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8s9f
Deposition date deposition_date2023-03-28
Structure title titleCrystal structure of the kinase domain of Bruton's Tyrosine Kinase bound to dasatinib
Keywords keywords;Bruton's Tyrosine Kinase, ATP-binding, protein phosphorylation, TRANSFERASE ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.95
Radius of gyration Rg (electron density) rg_electron27.02
Forward intensity I(0) i056827400.00
Molecular weight molecular_weight58405.0 kDa
Excluded volume excluded_volume72778 ų
Envelope volume envelope_volume92803 ų
Hydration-shell volume shell_volume29083 ų
Envelope diameter envelope_diameter88.0
Shell Rg shell_rg33.97
Envelope Rg envelope_rg26.53
Shape Rg shape_rg27.02
Total Rg total_rg27.75
Total atoms total_atoms7935
Residues n_residues509
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax90.2
Rg (real space) rg_real27.93
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real5.6830e+07
I(0) uncertainty (real space) i0_real_error7.6670e+05
Rg (reciprocal space) rg_reciprocal27.94
I(0) (reciprocal space) i0_reciprocal56830000.0000
Solution quality estimate total_estimate0.9029
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.259
Kurtosis Kurtosis kurtosis-0.546
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15820000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.951

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id8s9fA01
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_id8s9fA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id8s9fB01
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_id8s9fB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)