3bz3

Crystal Structure Analysis of Focal Adhesion Kinase with a Methanesulfonamide Diaminopyrimidine Inhibitor

Method: X-RAY DIFFRACTION Dmax: 65.8 Å Quality: REASONABLE

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

Focal adhesion kinase 1

Homo sapiens

UniProt Q05397

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 414–689 Fragment:kinase domain YAM N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;15% PEG 8000, 0.1M HEPES, 0.2M (NH4)2SO4, pH 7.5, vapor diffusion, temperature 298K Resolution 2.20 Å R-free 0.234

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.

38 other PDB entries and 81 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FAK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 414–689

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 3bz3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bz3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bz3
Deposition date deposition_date2008-01-17
Structure title titleCrystal Structure Analysis of Focal Adhesion Kinase with a Methanesulfonamide Diaminopyrimidine Inhibitor
Keywords keywords;kinase, DFG-helix, Acetylation, Alternative splicing, ATP-binding, Cell junction, Nucleotide-binding, Phosphoprotein, Transferase, Tyrosine-protein kinase ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.31
Radius of gyration Rg (electron density) rg_electron19.16
Forward intensity I(0) i016004000.00
Molecular weight molecular_weight30308.0 kDa
Excluded volume excluded_volume38027 ų
Envelope volume envelope_volume43624 ų
Hydration-shell volume shell_volume19232 ų
Envelope diameter envelope_diameter66.0
Shell Rg shell_rg25.39
Envelope Rg envelope_rg19.48
Shape Rg shape_rg19.16
Total Rg total_rg20.06
Total atoms total_atoms2126
Residues n_residues259
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 dmax65.8
Rg (real space) rg_real20.26
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real1.6000e+07
I(0) uncertainty (real space) i0_real_error2.0920e+05
Rg (reciprocal space) rg_reciprocal20.27
I(0) (reciprocal space) i0_reciprocal16000000.0000
Solution quality estimate total_estimate0.6316
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5
Skewness Skewness skewness0.298
Kurtosis Kurtosis kurtosis-0.386
Angular range angular_range— – 0.3900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4697000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 0.999; Sysdev: 0.193; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3bz3a_
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.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id3bz3A01
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_id3bz3A02
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)