4qps

Crystal structure of Jak3 complexed to N-[3-(6-Phenylamino-pyrazin-2-yl)-3H-benzoimidazol-5-yl]-acrylamide

Method: X-RAY DIFFRACTION Dmax: 86.9 Å Quality: EXCELLENT

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

Tyrosine-protein kinase JAK3

Homo sapiens

UniProt P52333

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 811–1103 Fragment:Jak3, unp residues 811-1103 Mutation:C1040S, C1048S, D949A 37Q N-{1-[6-(phenylamino)pyrazin-2-yl]-1H-benzimidazol-6-yl}prop-2-enamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.5;291 K;25% PEG-3350, 0.2 M ammonium sulfate and 0.1 M BisTRIS pH 5.5, VAPOR DIFFUSION, temperature 291K Resolution 1.80 Å R-free 0.251
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 811–1103 Fragment:Jak3, unp residues 811-1103 Mutation:C1040S, C1048S, D949A 37Q N-{1-[6-(phenylamino)pyrazin-2-yl]-1H-benzimidazol-6-yl}prop-2-enamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.5;291 K;25% PEG-3350, 0.2 M ammonium sulfate and 0.1 M BisTRIS pH 5.5, VAPOR DIFFUSION, temperature 291K Resolution 1.80 Å R-free 0.251

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.

41 other PDB entries and 69 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name JAK3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–293; UniProt 811–1103 Author chain C; PDBConstruct 1–293; UniProt 811–1103

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 4qps

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4qps
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4qps
Deposition date deposition_date2014-06-24
Structure title titleCrystal structure of Jak3 complexed to N-[3-(6-Phenylamino-pyrazin-2-yl)-3H-benzoimidazol-5-yl]-acrylamide
Keywords keywordsKinase catalytic domain, TRANSFERASE, Transferase-transferase inhibitor complex; Transferase/transferase inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.02
Radius of gyration Rg (electron density) rg_electron27.22
Forward intensity I(0) i062725600.00
Molecular weight molecular_weight62571.0 kDa
Excluded volume excluded_volume78618 ų
Envelope volume envelope_volume97869 ų
Hydration-shell volume shell_volume30276 ų
Envelope diameter envelope_diameter89.5
Shell Rg shell_rg34.19
Envelope Rg envelope_rg26.81
Shape Rg shape_rg27.20
Total Rg total_rg28.01
Total atoms total_atoms4406
Residues n_residues546
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 dmax86.9
Rg (real space) rg_real28.01
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real6.2730e+07
I(0) uncertainty (real space) i0_real_error7.4910e+05
Rg (reciprocal space) rg_reciprocal28.02
I(0) (reciprocal space) i0_reciprocal62730000.0000
Solution quality estimate total_estimate0.9070
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.0
Skewness Skewness skewness0.293
Kurtosis Kurtosis kurtosis-0.572
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22040000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.926

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4qpsa_
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
Domain ID domain_idd4qpsc_
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 (4 domains)

Domain ID domain_id4qpsA01
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_id4qpsA02
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_id4qpsC01
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_id4qpsC02
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)