6x8e

Crystal structure of JAK2 with Compound 11

Method: X-RAY DIFFRACTION Dmax: 95.1 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 837–1132 Fragment:kinase domain Mutation:M1073S, F1076T Non-standard monomer:Yes (specific site not provided by mmCIF) UWP [3-{4-[6-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrazin-4-yl]-1H-pyrazol-1-yl}-1-(2,2,2-trifluoroethyl)azetidin-3-yl]acetonitrile × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 7.5;298 K;0.1 M HEPES pH 7.5, 0.1 M sodium acetate trihydrate, and 30-35% PEG-3350 Resolution 1.75 Å R-free 0.225
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 837–1132 Fragment:kinase domain Mutation:M1073S, F1076T Non-standard monomer:Yes (specific site not provided by mmCIF) UWP [3-{4-[6-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrazin-4-yl]-1H-pyrazol-1-yl}-1-(2,2,2-trifluoroethyl)azetidin-3-yl]acetonitrile × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 7.5;298 K;0.1 M HEPES pH 7.5, 0.1 M sodium acetate trihydrate, and 30-35% PEG-3350 Resolution 1.75 Å R-free 0.225

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 3–298; UniProt 837–1132 Author chain B; PDBConstruct 3–298; UniProt 837–1132

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 6x8e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6x8e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6x8e
Deposition date deposition_date2020-06-01
Structure title titleCrystal structure of JAK2 with Compound 11
Keywords keywordskinase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.20
Radius of gyration Rg (electron density) rg_electron29.26
Forward intensity I(0) i072724900.00
Molecular weight molecular_weight66599.0 kDa
Excluded volume excluded_volume83241 ų
Envelope volume envelope_volume106220 ų
Hydration-shell volume shell_volume30695 ų
Envelope diameter envelope_diameter98.6
Shell Rg shell_rg36.01
Envelope Rg envelope_rg29.08
Shape Rg shape_rg29.23
Total Rg total_rg30.01
Total atoms total_atoms4718
Residues n_residues551
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 dmax95.1
Rg (real space) rg_real30.21
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real7.2720e+07
I(0) uncertainty (real space) i0_real_error1.1500e+06
Rg (reciprocal space) rg_reciprocal30.21
I(0) (reciprocal space) i0_reciprocal72720000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.264
Kurtosis Kurtosis kurtosis-0.655
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13730000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.913

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6x8ea_
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_idd6x8eb_
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

8. Citations (1)

9. Files and Curves (10)