6vnm

JAK2 JH1 in complex with SY5-103

Method: X-RAY DIFFRACTION Dmax: 92.3 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 B; UniProt 840–1132 Non-standard monomer:Yes (specific site not provided by mmCIF) R5Y 4-[1-(but-3-en-1-yl)-1H-pyrazol-4-yl]-N-[4-(piperidin-4-yl)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-2-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;291 K;0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350 Resolution 2.20 Å R-free 0.238
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 840–1132 Non-standard monomer:Yes (specific site not provided by mmCIF) R5Y 4-[1-(but-3-en-1-yl)-1H-pyrazol-4-yl]-N-[4-(piperidin-4-yl)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-2-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;291 K;0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350 Resolution 2.20 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 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 16–308; UniProt 840–1132 Author chain B; PDBConstruct 16–308; 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 6vnm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6vnm
Deposition date deposition_date2020-01-29
Structure title titleJAK2 JH1 in complex with SY5-103
Keywords keywordsjanus associated kinase, JAK2, kinase domain, JH1, kinase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.30
Radius of gyration Rg (electron density) rg_electron28.34
Forward intensity I(0) i079283400.00
Molecular weight molecular_weight69931.0 kDa
Excluded volume excluded_volume87634 ų
Envelope volume envelope_volume111970 ų
Hydration-shell volume shell_volume33123 ų
Envelope diameter envelope_diameter100.3
Shell Rg shell_rg35.36
Envelope Rg envelope_rg28.10
Shape Rg shape_rg28.32
Total Rg total_rg29.12
Total atoms total_atoms4922
Residues n_residues585
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 dmax92.3
Rg (real space) rg_real29.26
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real7.9280e+07
I(0) uncertainty (real space) i0_real_error9.6620e+05
Rg (reciprocal space) rg_reciprocal29.28
I(0) (reciprocal space) i0_reciprocal79280000.0000
Solution quality estimate total_estimate0.9104
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.5
Skewness Skewness skewness0.246
Kurtosis Kurtosis kurtosis-0.591
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23490000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.986

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd6vnma1
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_idd6vnma2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6vnmb_
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)