2rfe

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

Method: X-RAY DIFFRACTION Dmax: 118.7 Å Quality: GOOD

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 702–1022 Fragment:Protein kinase domain Mutation:K799E ERBB receptor feedback inhibitor 1 × 1 (Q9UJM3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;19% PEG3350, 100 mM NaNO3, 100 mM Bis-Tris propane, pH 7.5, vapor diffusion, hanging drop, temperature 293K Resolution 2.90 Å R-free 0.271
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 702–1022 Fragment:Protein kinase domain Mutation:K799E ERBB receptor feedback inhibitor 1 × 1 (Q9UJM3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;19% PEG3350, 100 mM NaNO3, 100 mM Bis-Tris propane, pH 7.5, vapor diffusion, hanging drop, temperature 293K Resolution 2.90 Å R-free 0.271
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 702–1022 Fragment:Protein kinase domain Mutation:K799E No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;19% PEG3350, 100 mM NaNO3, 100 mM Bis-Tris propane, pH 7.5, vapor diffusion, hanging drop, temperature 293K Resolution 2.90 Å R-free 0.271
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 702–1022 Fragment:Protein kinase domain Mutation:K799E No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;19% PEG3350, 100 mM NaNO3, 100 mM Bis-Tris propane, pH 7.5, vapor diffusion, hanging drop, temperature 293K Resolution 2.90 Å R-free 0.271

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 562 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 4–324; UniProt 702–1022 Author chain B; PDBConstruct 4–324; UniProt 702–1022 Author chain C; PDBConstruct 4–324; UniProt 702–1022 Author chain D; PDBConstruct 4–324; UniProt 702–1022

ERBB receptor feedback inhibitor 1

OrganismNot specified

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 E; UniProt 325–364 Fragment:sequence database residues, 325-364 Epidermal growth factor receptor × 1 (P00533) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;19% PEG3350, 100 mM NaNO3, 100 mM Bis-Tris propane, pH 7.5, vapor diffusion, hanging drop, temperature 293K Resolution 2.90 Å R-free 0.271
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 325–364 Fragment:sequence database residues, 325-364 Epidermal growth factor receptor × 1 (P00533) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;19% PEG3350, 100 mM NaNO3, 100 mM Bis-Tris propane, pH 7.5, vapor diffusion, hanging drop, temperature 293K Resolution 2.90 Å R-free 0.271

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 E; PDBConstruct 1–40; UniProt 325–364 Author chain F; PDBConstruct 1–40; UniProt 325–364

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 2rfe

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2rfe
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_guinier37.14
Radius of gyration Rg (electron density) rg_electron36.56
Forward intensity I(0) i0227208000.00
Molecular weight molecular_weight125850.0 kDa
Excluded volume excluded_volume159350 ų
Envelope volume envelope_volume215910 ų
Hydration-shell volume shell_volume49432 ų
Envelope diameter envelope_diameter120.3
Shell Rg shell_rg42.71
Envelope Rg envelope_rg35.53
Shape Rg shape_rg36.55
Total Rg total_rg37.04
Total atoms total_atoms8853
Residues n_residues1149
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 dmax118.7
Rg (real space) rg_real37.06
Rg uncertainty (real space) rg_real_error1.02
I(0) (real space) i0_real2.2720e+08
I(0) uncertainty (real space) i0_real_error3.9720e+06
Rg (reciprocal space) rg_reciprocal37.12
I(0) (reciprocal space) i0_reciprocal227200000.0000
Solution quality estimate total_estimate0.8948
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.9
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.472
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35290000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.829

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2rfed_
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 (8 domains)

Domain ID domain_id2rfeA01
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_id2rfeA02
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_id2rfeB01
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_id2rfeB02
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_id2rfeC01
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_id2rfeC02
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_id2rfeD01
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_id2rfeD02
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)