4fvp

Crystal structure of the Jak2 pseudokinase domain (apo form)

Method: X-RAY DIFFRACTION Dmax: 67.6 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 Fragment:Jak2 pseudokinase domain, UNP residues 536-812 Mutation:W659A, W777A, F794H GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;100 mM Tris/HCl, PEG 4000, pH 8.0, vapor diffusion, hanging drop, temperature 277K Resolution 2.01 Å R-free 0.212

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 251 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

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 4fvp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fvp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fvp
Deposition date deposition_date2012-06-29
Structure title titleCrystal structure of the Jak2 pseudokinase domain (apo form)
Keywords keywordsJANUS PROTEIN KINASE, PSEUDOKINASE, ATP BINDING, PHOSPHORYLATION, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.17
Radius of gyration Rg (electron density) rg_electron18.84
Forward intensity I(0) i016228500.00
Molecular weight molecular_weight30549.0 kDa
Excluded volume excluded_volume38349 ų
Envelope volume envelope_volume44826 ų
Hydration-shell volume shell_volume19837 ų
Envelope diameter envelope_diameter66.3
Shell Rg shell_rg25.36
Envelope Rg envelope_rg19.19
Shape Rg shape_rg18.86
Total Rg total_rg19.75
Total atoms total_atoms2152
Residues n_residues274
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 dmax67.6
Rg (real space) rg_real20.10
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real1.6230e+07
I(0) uncertainty (real space) i0_real_error2.0580e+05
Rg (reciprocal space) rg_reciprocal20.12
I(0) (reciprocal space) i0_reciprocal16230000.0000
Solution quality estimate total_estimate0.8799
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.1
Skewness Skewness skewness0.254
Kurtosis Kurtosis kurtosis-0.329
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4696000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4fvpa_
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 (2 domains)

Domain ID domain_id4fvpA01
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_id4fvpA02
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)