8ba4

Crystal structure of JAK2 JH2-V617F in complex with Bemcentinib

Method: X-RAY DIFFRACTION Dmax: 93.6 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 536–812 Mutation:W659A, W777A, F794H, V617F Q8U 1-(3,4-diazatricyclo[9.4.0.0^{2,7}]pentadeca-1(11),2(7),3,5,12,14-hexaen-5-yl)-~{N}3-[(7~{S})-7-pyrrolidin-1-yl-6,7,8,9-tetrahydro-5~{H}-benzo[7]annulen-3-yl]-1,2,4-triazole-3,5-diamine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.1M Tris pH 8, 20% PEG4000, 0.2M Na-acetate Resolution 2.10 Å R-free 0.274
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 536–812 Mutation:W659A, W777A, F794H, V617F No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.1M Tris pH 8, 20% PEG4000, 0.2M Na-acetate Resolution 2.10 Å R-free 0.274

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 1–277; UniProt 536–812 Author chain B; PDBConstruct 1–277; UniProt 536–812

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 8ba4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ba4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ba4
Deposition date deposition_date2022-10-11
Structure title titleCrystal structure of JAK2 JH2-V617F in complex with Bemcentinib
Keywords keywordsJanus kinase, pseudokinase, inhibitor complex, JAK2, JH2, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.26
Radius of gyration Rg (electron density) rg_electron27.39
Forward intensity I(0) i061150400.00
Molecular weight molecular_weight61770.0 kDa
Excluded volume excluded_volume77649 ų
Envelope volume envelope_volume97507 ų
Hydration-shell volume shell_volume30161 ų
Envelope diameter envelope_diameter97.3
Shell Rg shell_rg34.15
Envelope Rg envelope_rg27.32
Shape Rg shape_rg27.40
Total Rg total_rg28.10
Total atoms total_atoms8601
Residues n_residues548
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 dmax93.6
Rg (real space) rg_real28.27
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real6.1150e+07
I(0) uncertainty (real space) i0_real_error9.7710e+05
Rg (reciprocal space) rg_reciprocal28.27
I(0) (reciprocal space) i0_reciprocal61150000.0000
Solution quality estimate total_estimate0.8929
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.8
Skewness Skewness skewness0.334
Kurtosis Kurtosis kurtosis-0.404
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha15280000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.962

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id8ba4A01
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_id8ba4A02
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_id8ba4B01
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_id8ba4B02
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)