3lpb

Crystal structure of Jak2 complexed with a potent 2,8-diaryl-quinoxaline inhibitor

Method: X-RAY DIFFRACTION Dmax: 105.4 Å Quality: GOOD

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 840–1132 Fragment:Kinase domain Non-standard monomer:Yes (specific site not provided by mmCIF) NVB N-methyl-4-[3-(3,4,5-trimethoxyphenyl)quinoxalin-5-yl]benzenesulfonamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;298 K;30% PEG4000, 0.1M AMMONIUM SULFATE, 0.1M NA CITRATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.207
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 840–1132 Fragment:Kinase domain Non-standard monomer:Yes (specific site not provided by mmCIF) NVB N-methyl-4-[3-(3,4,5-trimethoxyphenyl)quinoxalin-5-yl]benzenesulfonamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;298 K;30% PEG4000, 0.1M AMMONIUM SULFATE, 0.1M NA CITRATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.207

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 250 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 3–295; UniProt 840–1132 Author chain B; PDBConstruct 3–295; UniProt 840–1132

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 3lpb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3lpb
Deposition date deposition_date2010-02-05
Structure title titleCrystal structure of Jak2 complexed with a potent 2,8-diaryl-quinoxaline inhibitor
Keywords keywords;Small molecule inhibitor, ATP site kinase inhibitor, Novartis product NVP-BLU040, ATP-binding, Chromosomal rearrangement, Disease mutation, Kinase, Membrane, Nucleotide-binding, Phosphoprotein, Polymorphism, Proto-oncogene, SH2 domain, 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_guinier29.98
Radius of gyration Rg (electron density) rg_electron29.70
Forward intensity I(0) i068396000.00
Molecular weight molecular_weight65679.0 kDa
Excluded volume excluded_volume82405 ų
Envelope volume envelope_volume102410 ų
Hydration-shell volume shell_volume30148 ų
Envelope diameter envelope_diameter109.4
Shell Rg shell_rg34.86
Envelope Rg envelope_rg30.09
Shape Rg shape_rg29.71
Total Rg total_rg30.16
Total atoms total_atoms4622
Residues n_residues562
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 dmax105.4
Rg (real space) rg_real30.19
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real6.8400e+07
I(0) uncertainty (real space) i0_real_error1.1460e+06
Rg (reciprocal space) rg_reciprocal30.10
I(0) (reciprocal space) i0_reciprocal68390000.0000
Solution quality estimate total_estimate0.8405
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.8
Skewness Skewness skewness0.527
Kurtosis Kurtosis kurtosis-0.250
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21360000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.809; Smooth: 0.963

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3lpba_
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_idd3lpbb1
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_idd3lpbb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id3lpbA01
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_id3lpbA02
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_id3lpbB01
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_id3lpbB02
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)