4zjv

crystal structure of EGFR kinase domain in complex with Mitogen-inducible gene 6 protein

Method: X-RAY DIFFRACTION Dmax: 104.1 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 695–1022 Fragment:Kinase domain (UNP residues 695-1022) ERBB receptor feedback inhibitor 1 × 1 (Q9UJM3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.1 M Bis-Tris 0.2 M Ammonium acetate 25% PEG3350 Resolution 2.70 Å R-free 0.232
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 695–1022 Fragment:Kinase domain (UNP residues 695-1022) ERBB receptor feedback inhibitor 1 × 1 (Q9UJM3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.1 M Bis-Tris 0.2 M Ammonium acetate 25% PEG3350 Resolution 2.70 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.

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 4–331; UniProt 695–1022 Author chain B; PDBConstruct 4–331; UniProt 695–1022

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 330–399 Fragment:UNP residues 330-399 Mutation:S390C Non-standard monomer:Yes (specific site not provided by mmCIF) Epidermal growth factor receptor × 1 (P00533) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.1 M Bis-Tris 0.2 M Ammonium acetate 25% PEG3350 Resolution 2.70 Å R-free 0.232
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 330–399 Fragment:UNP residues 330-399 Mutation:S390C Non-standard monomer:Yes (specific site not provided by mmCIF) Epidermal growth factor receptor × 1 (P00533) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;0.1 M Bis-Tris 0.2 M Ammonium acetate 25% PEG3350 Resolution 2.70 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.

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 1–70; UniProt 330–399 Author chain D; PDBConstruct 1–70; UniProt 330–399

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 4zjv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zjv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4zjv
Deposition date deposition_date2015-04-29
Structure title titlecrystal structure of EGFR kinase domain in complex with Mitogen-inducible gene 6 protein
Keywords keywords;Epidermal growth factor receptor (EGFR), ERBB receptor feedback inhibitor 1, Mitogen-inducible gene 6 protein(Mig6), TRANSFERASE-INHIBITOR complex ;; TRANSFERASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.94
Radius of gyration Rg (electron density) rg_electron31.63
Forward intensity I(0) i079195900.00
Molecular weight molecular_weight73679.0 kDa
Excluded volume excluded_volume93713 ų
Envelope volume envelope_volume119500 ų
Hydration-shell volume shell_volume32173 ų
Envelope diameter envelope_diameter106.6
Shell Rg shell_rg37.56
Envelope Rg envelope_rg31.61
Shape Rg shape_rg31.61
Total Rg total_rg32.25
Total atoms total_atoms5171
Residues n_residues643
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 dmax104.1
Rg (real space) rg_real32.12
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real7.9200e+07
I(0) uncertainty (real space) i0_real_error1.1820e+06
Rg (reciprocal space) rg_reciprocal32.05
I(0) (reciprocal space) i0_reciprocal79190000.0000
Solution quality estimate total_estimate0.8578
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.1
Skewness Skewness skewness0.367
Kurtosis Kurtosis kurtosis-0.712
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38870000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.867; Smooth: 0.873

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4zjvA01
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_id4zjvA02
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_id4zjvB01
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_id4zjvB02
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)