4g5p

Crystal structure of EGFR kinase T790M in complex with BIBW2992

Method: X-RAY DIFFRACTION Dmax: 104.8 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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 696–1022 Fragment:Kinase domain, UNP residues 696-1022 0WN N-{4-[(3-chloro-4-fluorophenyl)amino]-7-[(3S)-tetrahydrofuran-3-yloxy]quinazolin-6-yl}-4-(dimethylamino)butanamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.17 Å R-free 0.323
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 696–1022 Fragment:Kinase domain, UNP residues 696-1022 No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.17 Å R-free 0.323
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 696–1022 Chain B; UniProt 696–1022 Fragment:Kinase domain, UNP residues 696-1022 0WN N-{4-[(3-chloro-4-fluorophenyl)amino]-7-[(3S)-tetrahydrofuran-3-yloxy]quinazolin-6-yl}-4-(dimethylamino)butanamide × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.17 Å R-free 0.323

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 563 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

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 4g5p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4g5p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4g5p
Deposition date deposition_date2012-07-18
Structure title titleCrystal structure of EGFR kinase T790M in complex with BIBW2992
Keywords keywordsEGF RECEPTOR KINASE MUTANT T790M, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.57
Radius of gyration Rg (electron density) rg_electron30.55
Forward intensity I(0) i0142170000.00
Molecular weight molecular_weight64244.0 kDa
Excluded volume excluded_volume62573 ų
Envelope volume envelope_volume111140 ų
Hydration-shell volume shell_volume32076 ų
Envelope diameter envelope_diameter110.6
Shell Rg shell_rg35.55
Envelope Rg envelope_rg30.75
Shape Rg shape_rg30.55
Total Rg total_rg30.87
Total atoms total_atoms4864
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 dmax104.8
Rg (real space) rg_real30.87
Rg uncertainty (real space) rg_real_error0.90
I(0) (real space) i0_real1.4220e+08
I(0) uncertainty (real space) i0_real_error2.1330e+06
Rg (reciprocal space) rg_reciprocal30.75
I(0) (reciprocal space) i0_reciprocal142200000.0000
Solution quality estimate total_estimate0.8225
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.2
Skewness Skewness skewness0.579
Kurtosis Kurtosis kurtosis-0.238
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26650000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.747; Smooth: 0.791

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_idd4g5pa_
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_idd4g5pb_
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_id4g5pA01
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_id4g5pA02
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_id4g5pB01
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_id4g5pB02
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)