› 4krl

X-ray diffraction
2.85Å resolution

Nanobody/VHH domain 7D12 in complex with domain III of the extracellular region of EGFR, pH 6.0

Released:
DOI: 10.2210/pdb4krl/pdb
PDB entry 4krl coloured by chain, front view.
PDB entry 4krl coloured by chain, side view.
PDB entry 4krl coloured by chain, top view.
Source organisms:
Primary publication:
Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains.
Schmitz KR, Bagchi A, Roovers RC, van Bergen en Henegouwen PM, Ferguson KM
Structure 21 1214-24 (2013)
PMID: 23791944

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 analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208217 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Nanobody/VHH domain 7D12 Chain: B
Molecule details ›
Chain: B
Length: 133 amino acids
Theoretical weight: 14.58 KDa
Source organism: Lama glama
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Epidermal growth factor receptor Chain: A
Molecule details ›
Chain: A
Length: 214 amino acids
Theoretical weight: 23.79 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
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
Carbohydrate polymer
3 bound ligands:
Ligand MES 2 x MES
Ligand NAG 2 x NAG
Ligand IOD 1 x IOD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P6122
Unit cell:
a: 148.048Å b: 148.048Å c: 82.51Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.213 0.268
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda

Quick links

Citations

20 review citations

Nanobodies and Nanobody-Based Human Heavy Chain Antibodies As Antitumor Therapeutics.
Bannas et al. (2017)
19 more

16 mentions without citation

Molecular Targeting of Epidermal Growth Factor Receptor (EGFR) and Vascular Endothelial Growth Factor Receptor (VEGFR).
Kaufman et al. (2021)
15 more