5hez

JAK2 kinase (JH1 domain) mutant P1057A in complex with TG101209

Method: X-RAY DIFFRACTION Dmax: 117.5 Å Quality: EXCELLENT

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

Tyrosine-protein kinase JAK2

Homo sapiens

UniProt O60674

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 833–1132 Mutation:P1057A Non-standard monomer:Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 ZN ZINC ION × 1 1M3 N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;1.9 M sodium malonate, 10 mM ZnCl2 Resolution 2.66 Å R-free 0.238
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 833–1132 Mutation:P1057A Non-standard monomer:Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 ZN ZINC ION × 1 1M3 N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;1.9 M sodium malonate, 10 mM ZnCl2 Resolution 2.66 Å R-free 0.238
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 833–1132 Mutation:P1057A Non-standard monomer:Yes (specific site not provided by mmCIF) 1M3 N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;1.9 M sodium malonate, 10 mM ZnCl2 Resolution 2.66 Å R-free 0.238
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 833–1132 Mutation:P1057A Non-standard monomer:Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 1M3 N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;1.9 M sodium malonate, 10 mM ZnCl2 Resolution 2.66 Å R-free 0.238
5 Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 833–1132 Chain B; UniProt 833–1132 Chain C; UniProt 833–1132 Chain D; UniProt 833–1132 Mutation:P1057A Non-standard monomer:Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 6 ZN ZINC ION × 4 1M3 N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide × 16 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;1.9 M sodium malonate, 10 mM ZnCl2 Resolution 2.66 Å R-free 0.238

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.

161 other PDB entries and 247 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name JAK2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–302; UniProt 833–1132 Author chain B; PDBConstruct 3–302; UniProt 833–1132 Author chain C; PDBConstruct 3–302; UniProt 833–1132 Author chain D; PDBConstruct 3–302; UniProt 833–1132

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 5hez

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5hez
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5hez
Deposition date deposition_date2016-01-06
Structure title titleJAK2 kinase (JH1 domain) mutant P1057A in complex with TG101209
Keywords keywordsprotein kinase, inhibitor, mutation, TYK2, surrogate, P1104A, 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_guinier36.98
Radius of gyration Rg (electron density) rg_electron36.12
Forward intensity I(0) i0306475000.00
Molecular weight molecular_weight141270.0 kDa
Excluded volume excluded_volume176610 ų
Envelope volume envelope_volume234070 ų
Hydration-shell volume shell_volume53080 ų
Envelope diameter envelope_diameter119.6
Shell Rg shell_rg43.53
Envelope Rg envelope_rg35.42
Shape Rg shape_rg36.10
Total Rg total_rg36.67
Total atoms total_atoms9914
Residues n_residues1154
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 dmax117.5
Rg (real space) rg_real36.86
Rg uncertainty (real space) rg_real_error1.00
I(0) (real space) i0_real3.0650e+08
I(0) uncertainty (real space) i0_real_error5.2010e+06
Rg (reciprocal space) rg_reciprocal36.94
I(0) (reciprocal space) i0_reciprocal306500000.0000
Solution quality estimate total_estimate0.9007
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.2
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.534
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha145600000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.899

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5heza_
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_idd5hezb_
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_idd5hezc_
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_idd5hezd_
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 (8 domains)

Domain ID domain_id5hezA01
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_id5hezA02
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_id5hezB01
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_id5hezB02
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_id5hezC01
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_id5hezC02
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_id5hezD01
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_id5hezD02
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)