› 4krp

X-ray diffraction
2.82Å resolution

Nanobody/VHH domain 9G8 in complex with the extracellular region of EGFR

Released:
DOI: 10.2210/pdb4krp/pdb
PDB entry 4krp coloured by chain, front view.
PDB entry 4krp coloured by chain, side view.
PDB entry 4krp 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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208220 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Epidermal growth factor receptor Chain: A
Molecule details ›
Chain: A
Length: 625 amino acids
Theoretical weight: 69.3 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P00533 (Residues: 25-637, 638-642; Coverage: 52%)
Gene names: EGFR, ERBB, ERBB1, HER1
Sequence domains:
Structure domains:
Nanobody/VHH domain 9G8 Chain: B
Molecule details ›
Chain: B
Length: 136 amino acids
Theoretical weight: 15.18 KDa
Source organism: Lama glama
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Cetuximab light chain Chain: C
Molecule details ›
Chain: C
Length: 211 amino acids
Theoretical weight: 23.16 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Structure domains: Immunoglobulins
Cetuximab heavy chain Chain: D
Molecule details ›
Chain: D
Length: 220 amino acids
Theoretical weight: 23.64 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 4 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 66.372Å b: 95.841Å c: 129.481Å
α: 90° β: 99.95° γ: 90°
R-values:
R R work R free
0.218 0.215 0.263
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli
  • Mus musculus

Quick links

Citations

22 review citations

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

14 mentions without citation

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