3c09

Crystal structure the Fab fragment of matuzumab (Fab72000) in complex with domain III of the extracellular region of EGFR

Method: X-RAY DIFFRACTION Dmax: 124.6 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 336–538 Fragment:sEGFR domain III Matuzumab Fab Light chain × 1 Matuzumab Fab Heavy chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 BMA beta-D-mannopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;298 K;16% PEG 3350, 1M NaCl, pH 6.0, vapor diffusion, temperature 298K Resolution 3.20 Å R-free 0.299
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 336–538 Fragment:sEGFR domain III Matuzumab Fab Light chain × 1 Matuzumab Fab Heavy chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 BMA beta-D-mannopyranose × 1 MAN alpha-D-mannopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;298 K;16% PEG 3350, 1M NaCl, pH 6.0, vapor diffusion, temperature 298K Resolution 3.20 Å R-free 0.299

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 3
Chains and sequence ranges Author chain A; PDBConstruct 6–208; UniProt 336–538 Author chain D; PDBConstruct 6–208; UniProt 336–538

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 3c09

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3c09
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3c09
Deposition date deposition_date2008-01-18
Structure title titleCrystal structure the Fab fragment of matuzumab (Fab72000) in complex with domain III of the extracellular region of EGFR
Keywords keywords;CELL SURFACE RECEPTOR, GLYCOPROTEIN, ANTIGEN, ANTIBODY COMPLEX, FAB FRAGMENT, ANTITUMOR, DRUG IMMUNE SYSTEM-TRANSFERASE COMPLEX, IMMUNE SYSTEM-TRANSFERASE complex ;; IMMUNE SYSTEM/TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.00
Radius of gyration Rg (electron density) rg_electron37.37
Forward intensity I(0) i0243966000.00
Molecular weight molecular_weight121000.0 kDa
Excluded volume excluded_volume148620 ų
Envelope volume envelope_volume211610 ų
Hydration-shell volume shell_volume46808 ų
Envelope diameter envelope_diameter124.7
Shell Rg shell_rg43.47
Envelope Rg envelope_rg37.23
Shape Rg shape_rg37.37
Total Rg total_rg37.76
Total atoms total_atoms8532
Residues n_residues1175
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 dmax124.6
Rg (real space) rg_real37.90
Rg uncertainty (real space) rg_real_error0.89
I(0) (real space) i0_real2.4400e+08
I(0) uncertainty (real space) i0_real_error4.3630e+06
Rg (reciprocal space) rg_reciprocal37.96
I(0) (reciprocal space) i0_reciprocal244000000.0000
Solution quality estimate total_estimate0.8987
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.5
Skewness Skewness skewness0.191
Kurtosis Kurtosis kurtosis-0.505
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha17340000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd3c09a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.2 — L domain-like
Family Family familyc.10.2.5 — L domain
Domain ID domain_idd3c09a2
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.9 — Growth factor receptor domain
Family Family familyg.3.9.1 — Growth factor receptor domain
Domain ID domain_idd3c09a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3c09c1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3c09c2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3c09d1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.2 — L domain-like
Family Family familyc.10.2.5 — L domain
Domain ID domain_idd3c09d2
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.9 — Growth factor receptor domain
Family Family familyg.3.9.1 — Growth factor receptor domain
Domain ID domain_idd3c09d3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3c09h1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3c09h2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (10 domains)

Domain ID domain_id3c09A00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id3c09B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3c09B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3c09C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3c09C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3c09D00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id3c09H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3c09H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3c09L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3c09L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)