2rf9

Crystal structure of the complex between the EGFR kinase domain and a Mig6 peptide

Method: X-RAY DIFFRACTION Dmax: 121.4 Å Quality: REASONABLE

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

Epidermal growth factor receptor

Homo sapiens

UniProt P00533

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 696–1022 Fragment:Protein kinase domain ERBB receptor feedback inhibitor 1 × 1 (Q9UJM3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;293 K;20% PEG3350, 300 mM KAC, 10% Glycerol and 100 mM NaAc, pH 5.0, vapor diffusion, hanging drop, temperature 293K Resolution 3.50 Å R-free 0.329
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 696–1022 Fragment:Protein kinase domain ERBB receptor feedback inhibitor 1 × 1 (Q9UJM3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;293 K;20% PEG3350, 300 mM KAC, 10% Glycerol and 100 mM NaAc, pH 5.0, vapor diffusion, hanging drop, temperature 293K Resolution 3.50 Å R-free 0.329

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.

383 other PDB entries and 564 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGFR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–330; UniProt 696–1022 Author chain B; PDBConstruct 4–330; UniProt 696–1022

ERBB receptor feedback inhibitor 1

Homo sapiens

UniProt Q9UJM3

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 C; UniProt 315–374 Fragment:sequence database residues, 315-374 Epidermal growth factor receptor × 1 (P00533) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;293 K;20% PEG3350, 300 mM KAC, 10% Glycerol and 100 mM NaAc, pH 5.0, vapor diffusion, hanging drop, temperature 293K Resolution 3.50 Å R-free 0.329
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 315–374 Fragment:sequence database residues, 315-374 Epidermal growth factor receptor × 1 (P00533) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;293 K;20% PEG3350, 300 mM KAC, 10% Glycerol and 100 mM NaAc, pH 5.0, vapor diffusion, hanging drop, temperature 293K Resolution 3.50 Å R-free 0.329

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.

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ERRFI_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 6–65; UniProt 315–374 Author chain D; PDBConstruct 6–65; UniProt 315–374

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 2rf9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2rf9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2rf9
Deposition date deposition_date2007-09-28
Structure title titleCrystal structure of the complex between the EGFR kinase domain and a Mig6 peptide
Keywords keywords;kinase domain, inhibition, dimer, Alternative splicing, Anti-oncogene, ATP-binding, Cell cycle, Disease mutation, Glycoprotein, Membrane, Nucleotide-binding, Phosphorylation, Polymorphism, Receptor, Secreted, Transferase, Transmembrane, Tyrosine-protein kinase, Ubl conjugation, Cytoplasm ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.12
Radius of gyration Rg (electron density) rg_electron32.37
Forward intensity I(0) i059879100.00
Molecular weight molecular_weight62972.0 kDa
Excluded volume excluded_volume79423 ų
Envelope volume envelope_volume102220 ų
Hydration-shell volume shell_volume28363 ų
Envelope diameter envelope_diameter128.8
Shell Rg shell_rg35.89
Envelope Rg envelope_rg33.17
Shape Rg shape_rg32.39
Total Rg total_rg32.59
Total atoms total_atoms4435
Residues n_residues602
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 dmax121.4
Rg (real space) rg_real32.71
Rg uncertainty (real space) rg_real_error1.61
I(0) (real space) i0_real5.9880e+07
I(0) uncertainty (real space) i0_real_error9.7890e+05
Rg (reciprocal space) rg_reciprocal32.46
I(0) (reciprocal space) i0_reciprocal59870000.0000
Solution quality estimate total_estimate0.7259
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3
Skewness Skewness skewness0.689
Kurtosis Kurtosis kurtosis-0.086
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23940000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.396; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.321; Smooth: 0.924

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id2rf9A01
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_id2rf9A02
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_id2rf9B01
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_id2rf9B02
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)