8s93

Crystal structure of the PH-TH/kinase complex of Bruton's tyrosine kinase

Method: X-RAY DIFFRACTION Dmax: 93.0 Å Quality: GOOD

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–171 Chain A; UniProt 396–659 Fragment:PHTH domain residues 1-171 and Kinase domain residues 396-659 Mutation:Q91A, I92A, I94A, I95A, K430R, L542M S543T, V555T, R562K, S564A, P565S, Y617P 9AJ 2-[3'-(hydroxymethyl)-1-methyl-5-({5-[(2S)-2-methyl-4-(oxetan-3-yl)piperazin-1-yl]pyridin-2-yl}amino)-6-oxo[1,6-dihydro[3,4'-bipyridine]]-2'-yl]-7,7-dimethyl-3,4,7,8-tetrahydro-2H-cyclopenta[4,5]pyrrolo[1,2-a]pyrazin-1(6H)-one × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.6;277 K;20%PEG3350, 0.1M Bis-Tris, pH5.6, 0.2M magnesium chloride Resolution 2.10 Å R-free 0.246

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 1–171; UniProt 1–171 Author chain A; PDBConstruct 194–457; UniProt 396–659

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 8s93

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8s93
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8s93
Deposition date deposition_date2023-03-27
Structure title titleCrystal structure of the PH-TH/kinase complex of Bruton's tyrosine kinase
Keywords keywords;Bruton's tyrosine kinase, Non-receptor tyrosine kinase, complex, lipid-binding, ATP-binding, TRANSFERASE ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.76
Radius of gyration Rg (electron density) rg_electron26.08
Forward intensity I(0) i041126300.00
Molecular weight molecular_weight50169.0 kDa
Excluded volume excluded_volume62969 ų
Envelope volume envelope_volume77300 ų
Hydration-shell volume shell_volume25579 ų
Envelope diameter envelope_diameter95.1
Shell Rg shell_rg32.42
Envelope Rg envelope_rg26.54
Shape Rg shape_rg26.11
Total Rg total_rg26.71
Total atoms total_atoms6973
Residues n_residues429
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 dmax93.0
Rg (real space) rg_real26.92
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real4.1130e+07
I(0) uncertainty (real space) i0_real_error5.9840e+05
Rg (reciprocal space) rg_reciprocal26.88
I(0) (reciprocal space) i0_reciprocal41120000.0000
Solution quality estimate total_estimate0.8431
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.8
Skewness Skewness skewness0.501
Kurtosis Kurtosis kurtosis-0.267
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12520000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.770; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id8s93A01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id8s93A02
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_id8s93A03
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)