6glb

Crystal structure of JAK3 in complex with Compound 20 (FM484)

Method: X-RAY DIFFRACTION Dmax: 92.9 Å Quality: GOOD

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 812–1103 Not recorded F48 3-[5-(3-cyclohexyl-3,5,8,10-tetrazatricyclo[7.3.0.0^{2,6}]dodeca-1(9),2(6),4,7,11-pentaen-4-yl)furan-2-yl]propanenitrile × 1 PHU 1-phenylurea × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;24-30% PEG 3350, 0.1 M MES, pH 5.5-6.0 and 0.1-0.2 M MgCl2 Resolution 2.00 Å R-free 0.290
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 812–1103 Not recorded F48 3-[5-(3-cyclohexyl-3,5,8,10-tetrazatricyclo[7.3.0.0^{2,6}]dodeca-1(9),2(6),4,7,11-pentaen-4-yl)furan-2-yl]propanenitrile × 1 PHU 1-phenylurea × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;24-30% PEG 3350, 0.1 M MES, pH 5.5-6.0 and 0.1-0.2 M MgCl2 Resolution 2.00 Å R-free 0.290

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 3–294; UniProt 812–1103 Author chain B; PDBConstruct 3–294; UniProt 812–1103

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 6glb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6glb
Deposition date deposition_date2018-05-23
Structure title titleCrystal structure of JAK3 in complex with Compound 20 (FM484)
Keywords keywords;KINASE, JAK3, COVALENT INHIBITOR, REVERSIBLE COVALENT INHIBITOR, INDUCED POCKET, ARGININE POCKET, STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSFERASE ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.12
Radius of gyration Rg (electron density) rg_electron27.15
Forward intensity I(0) i071635800.00
Molecular weight molecular_weight66382.0 kDa
Excluded volume excluded_volume83225 ų
Envelope volume envelope_volume101700 ų
Hydration-shell volume shell_volume31549 ų
Envelope diameter envelope_diameter96.0
Shell Rg shell_rg34.09
Envelope Rg envelope_rg27.01
Shape Rg shape_rg27.14
Total Rg total_rg27.91
Total atoms total_atoms4674
Residues n_residues576
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 dmax92.9
Rg (real space) rg_real28.07
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real7.1640e+07
I(0) uncertainty (real space) i0_real_error8.6270e+05
Rg (reciprocal space) rg_reciprocal28.09
I(0) (reciprocal space) i0_reciprocal71640000.0000
Solution quality estimate total_estimate0.8971
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.267
Kurtosis Kurtosis kurtosis-0.483
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha15580000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6glba_
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_idd6glbb_
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_id6glbA01
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_id6glbA02
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_id6glbB01
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_id6glbB02
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)