› 3b2u

X-ray diffraction
2.58Å resolution

Crystal structure of isolated domain III of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of IMC-11F8

Released:
DOI: 10.2210/pdb3b2u/pdb
PDB entry 3b2u coloured by chain, front view.
PDB entry 3b2u coloured by chain, side view.
PDB entry 3b2u coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for EGF receptor inhibition by the therapeutic antibody IMC-11F8.
Li S, Kussie P, Ferguson KM
Structure 16 216-27 (2008)
PMID: 18275813

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-208210 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (7 distinct):
IMC-11F8 Fab Light chain Chains: D, G, K, L, O, R, U, X
Molecule details ›
Chains: D, G, K, L, O, R, U, X
Length: 213 amino acids
Theoretical weight: 23.05 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chains: C, F, H, J, N, Q, T, W
Molecule details ›
Chains: C, F, H, J, N, Q, T, W
Length: 223 amino acids
Theoretical weight: 23.6 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
UniProt:
  • Canonical: Q6GMX6 (Residues: 20-50, 51-116, 117-237; Coverage: 49%)
Gene name: IGH@
Sequence domains:
Structure domains: Immunoglobulins
Epidermal growth factor receptor Chains: A, B, E, I, M, P, S, V
Molecule details ›
Chains: A, B, E, I, M, P, S, V
Length: 214 amino acids
Theoretical weight: 23.79 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
UniProt:
  • Canonical: P00533 (Residues: 335-538; Coverage: 17%)
Gene names: EGFR, ERBB, ERBB1, HER1
Sequence domains: Receptor L domain
Structure domains: Receptor L-domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
2 bound ligands:
Ligand NAG 14 x NAG
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F2
Spacegroup: P21
Unit cell:
a: 154.373Å b: 139.122Å c: 175.325Å
α: 90° β: 90.02° γ: 90°
R-values:
R R work R free
0.23 0.227 0.291
Expression systems:
  • Spodoptera frugiperda
  • Mus musculus

Quick links

Citations

32 review citations

Phage display-derived human antibodies in clinical development and therapy.
Frenzel et al. (2016)
31 more

10 mentions without citation

Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains.
Schmitz et al. (2013)
9 more