6i8z

Crystal structure of PTK2 in complex with BI-4464.

Method: X-RAY DIFFRACTION Dmax: 82.4 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 411–689 Not recorded H82 3-methoxy-~{N}-(1-methylpiperidin-1-ium-4-yl)-4-[[4-[(3-oxidanylidene-1,2-dihydroinden-4-yl)oxy]-5-(trifluoromethyl)pyrimidin-2-yl]amino]benzamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;277 K;7%PEG1500, 100 mM SPG buffer, 5 mg/mL Resolution 1.99 Å R-free 0.222

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 Q05397-5
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–281; UniProt 411–689

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 6i8z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6i8z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6i8z
Deposition date deposition_date2018-11-21
Structure title titleCrystal structure of PTK2 in complex with BI-4464.
Keywords keywordsInhibitor, Protein kinase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.51
Radius of gyration Rg (electron density) rg_electron19.35
Forward intensity I(0) i016027300.00
Molecular weight molecular_weight30476.0 kDa
Excluded volume excluded_volume38294 ų
Envelope volume envelope_volume44843 ų
Hydration-shell volume shell_volume19538 ų
Envelope diameter envelope_diameter66.9
Shell Rg shell_rg25.59
Envelope Rg envelope_rg19.71
Shape Rg shape_rg19.35
Total Rg total_rg20.26
Total atoms total_atoms4274
Residues n_residues261
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 dmax82.4
Rg (real space) rg_real20.47
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real1.6030e+07
I(0) uncertainty (real space) i0_real_error2.4060e+05
Rg (reciprocal space) rg_reciprocal20.48
I(0) (reciprocal space) i0_reciprocal16030000.0000
Solution quality estimate total_estimate0.7059
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.4
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_alpha5605000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.464; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.779; 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_idd6i8za_
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_id6i8zA01
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_id6i8zA02
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)