6c7y

Crystal structure of inhibitory protein SOCS1 in complex with JAK1 kinase domain

Method: X-RAY DIFFRACTION Dmax: 80.2 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tyrosine-protein kinase JAK1

Homo sapiens

UniProt P23458

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 869–1153 Fragment:kinase domain (UNP residues 869-1153) Non-standard monomer:Yes (specific site not provided by mmCIF) Suppressor of cytokine signaling 1 × 1 (B6RCQ2) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;281 K;100mM HEPES pH 7.0, 14% (w/v) PEG8000, 100mM magnesium acetate, 2mM TCEP Resolution 2.50 Å R-free 0.241

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.

49 other PDB entries and 85 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name JAK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–286; UniProt 869–1153

Suppressor of cytokine signaling 1

Gallus gallus

UniProt B6RCQ2

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 48–164 Fragment:UNP residues 48-164 Tyrosine-protein kinase JAK1 × 1 (P23458) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;281 K;100mM HEPES pH 7.0, 14% (w/v) PEG8000, 100mM magnesium acetate, 2mM TCEP Resolution 2.50 Å R-free 0.241

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name B6RCQ2_CHICK
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–117; UniProt 48–164

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 6c7y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6c7y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6c7y
Deposition date deposition_date2018-01-23
Structure title titleCrystal structure of inhibitory protein SOCS1 in complex with JAK1 kinase domain
Keywords keywordsKinase, Kinase Inhibitor, SIGNALING PROTEIN, TRANSFERASE-INHIBITOR complex; SIGNALING PROTEIN, TRANSFERASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.23
Radius of gyration Rg (electron density) rg_electron23.54
Forward intensity I(0) i032938200.00
Molecular weight molecular_weight43998.0 kDa
Excluded volume excluded_volume54936 ų
Envelope volume envelope_volume66408 ų
Hydration-shell volume shell_volume24135 ų
Envelope diameter envelope_diameter82.1
Shell Rg shell_rg30.11
Envelope Rg envelope_rg23.96
Shape Rg shape_rg23.56
Total Rg total_rg24.25
Total atoms total_atoms3091
Residues n_residues390
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 dmax80.2
Rg (real space) rg_real24.29
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real3.2940e+07
I(0) uncertainty (real space) i0_real_error4.2330e+05
Rg (reciprocal space) rg_reciprocal24.28
I(0) (reciprocal space) i0_reciprocal32940000.0000
Solution quality estimate total_estimate0.8787
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.1
Skewness Skewness skewness0.408
Kurtosis Kurtosis kurtosis-0.377
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12410000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.947

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6c7ya1
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_idd6c7ya2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id6c7yA01
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_id6c7yA02
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)