› 4krm

X-ray diffraction
2.66Å resolution

Nanobody/VHH domain 7D12 in complex with domain III of the extracellular region of EGFR, pH 3.5

Released:
DOI: 10.2210/pdb4krm/pdb
PDB entry 4krm coloured by chain, front view.
PDB entry 4krm coloured by chain, side view.
PDB entry 4krm 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-208218 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Epidermal growth factor receptor Chains: A, C, E, G, I, K
Molecule details ›
Chains: A, C, E, G, I, K
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
Nanobody/VHH domain 7D12 Chains: B, D, F, H, J, L
Molecule details ›
Chains: B, D, F, H, J, L
Length: 133 amino acids
Theoretical weight: 14.58 KDa
Source organism: Lama glama
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 11 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 78.702Å b: 147.245Å c: 254.799Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.244
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli

Quick links

Citations

22 review citations

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

4 mentions without citation

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