3eta

Kinase domain of insulin receptor complexed with a pyrrolo pyridine inhibitor

Method: X-RAY DIFFRACTION Dmax: 98.2 Å Quality: GOOD

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

insulin receptor, kinase domain

Homo sapiens

UniProt P06213

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 1017–1322 Fragment:kinase domain 351 1-(3-{5-[4-(aminomethyl)phenyl]-1H-pyrrolo[2,3-b]pyridin-3-yl}phenyl)-3-(2-phenoxyphenyl)urea × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;295 K;0.1 M MOPS pH 7.0, 1.1 M sodium citrate, 1% Jeffamine M89, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.60 Å R-free 0.232
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1017–1322 Fragment:kinase domain 351 1-(3-{5-[4-(aminomethyl)phenyl]-1H-pyrrolo[2,3-b]pyridin-3-yl}phenyl)-3-(2-phenoxyphenyl)urea × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;295 K;0.1 M MOPS pH 7.0, 1.1 M sodium citrate, 1% Jeffamine M89, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.60 Å R-free 0.232
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1017–1322 Chain B; UniProt 1017–1322 Fragment:kinase domain 351 1-(3-{5-[4-(aminomethyl)phenyl]-1H-pyrrolo[2,3-b]pyridin-3-yl}phenyl)-3-(2-phenoxyphenyl)urea × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;295 K;0.1 M MOPS pH 7.0, 1.1 M sodium citrate, 1% Jeffamine M89, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.60 Å R-free 0.232

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.

85 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INSR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 12–317; UniProt 1017–1322 Author chain B; PDBConstruct 12–317; UniProt 1017–1322

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 3eta

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3eta
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3eta
Deposition date deposition_date2008-10-07
Structure title titleKinase domain of insulin receptor complexed with a pyrrolo pyridine inhibitor
Keywords keywords;ATP-binding, Carbohydrate metabolism, Cleavage on pair of basic residues, Diabetes mellitus, Disease mutation, Glycoprotein, Kinase, Membrane, Nucleotide-binding, Phosphoprotein, Receptor, Transferase, Transmembrane, Tyrosine-protein kinase, SIGNALING PROTEIN ;; SIGNALING PROTEIN, TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.45
Radius of gyration Rg (electron density) rg_electron29.70
Forward intensity I(0) i070084100.00
Molecular weight molecular_weight66202.0 kDa
Excluded volume excluded_volume82863 ų
Envelope volume envelope_volume106270 ų
Hydration-shell volume shell_volume30036 ų
Envelope diameter envelope_diameter99.9
Shell Rg shell_rg36.74
Envelope Rg envelope_rg29.19
Shape Rg shape_rg29.71
Total Rg total_rg30.32
Total atoms total_atoms4651
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 dmax98.2
Rg (real space) rg_real30.51
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real7.0080e+07
I(0) uncertainty (real space) i0_real_error9.9290e+05
Rg (reciprocal space) rg_reciprocal30.49
I(0) (reciprocal space) i0_reciprocal70080000.0000
Solution quality estimate total_estimate0.8809
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4
Skewness Skewness skewness0.289
Kurtosis Kurtosis kurtosis-0.707
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25910000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.891; Smooth: 0.924

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3etaa_
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.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd3etab_
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.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (4 domains)

Domain ID domain_id3etaA01
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_id3etaA02
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_id3etaB01
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_id3etaB02
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)