7t4j

Crystal Structure of EGFR_D770_N771insNPG/V948R in complex with TAK-788

Method: X-RAY DIFFRACTION Dmax: 92.0 Å Quality: EXCELLENT

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 696–1022 Chain B; UniProt 696–1022 Mutation:V948R R28 propan-2-yl 2-[[4-[2-(dimethylamino)ethyl-methyl-amino]-2-methoxy-5-(propanoylamino)phenyl]amino]-4-(1-methylindol-3-yl)pyrimidine-5-carboxylate × 2 EDO 1,2-ETHANEDIOL × 1 CIT CITRIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG 8000, 200mM Ammonium Citrate, 100mM MES pH 6.5 Resolution 2.20 Å R-free 0.278

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 565 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 2–331; UniProt 696–1022 Author chain B; PDBConstruct 2–331; UniProt 696–1022

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 7t4j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7t4j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7t4j
Deposition date deposition_date2021-12-10
Structure title titleCrystal Structure of EGFR_D770_N771insNPG/V948R in complex with TAK-788
Keywords keywordsKinase, Inhibitor, covalent, HYDROLASE, HYDROLASE-HYDROLASE Inhibitor complex; HYDROLASE/HYDROLASE Inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.53
Radius of gyration Rg (electron density) rg_electron27.75
Forward intensity I(0) i064181800.00
Molecular weight molecular_weight65231.0 kDa
Excluded volume excluded_volume82909 ų
Envelope volume envelope_volume102820 ų
Hydration-shell volume shell_volume31130 ų
Envelope diameter envelope_diameter96.5
Shell Rg shell_rg34.64
Envelope Rg envelope_rg27.53
Shape Rg shape_rg27.73
Total Rg total_rg28.57
Total atoms total_atoms4586
Residues n_residues557
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 dmax92.0
Rg (real space) rg_real28.52
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real6.4180e+07
I(0) uncertainty (real space) i0_real_error9.1170e+05
Rg (reciprocal space) rg_reciprocal28.53
I(0) (reciprocal space) i0_reciprocal64180000.0000
Solution quality estimate total_estimate0.9010
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6
Skewness Skewness skewness0.273
Kurtosis Kurtosis kurtosis-0.595
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21870000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.971

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7t4jA01
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_id7t4jA02
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_id7t4jB01
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_id7t4jB02
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)