5T1L image
Entry Detail
PDB ID:
5T1L
Keywords:
Title:
Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide
Biological Source:
PDB Version:
Deposition Date:
2016-08-19
Release Date:
2016-10-26
Method Details:
Experimental Method:
Resolution:
2.48 Å
R-Value Free:
0.20
R-Value Work:
0.15
R-Value Observed:
0.16
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:CETUXIMAB FAB LIGHT CHAIN
Chain IDs:A, C
Chain Length:213
Number of Molecules:2
Biological Source:Mus musculus, Homo sapiens
Polymer Type:polypeptide(L)
Description:CETUXIMAB FAB HEAVY CHAIN
Chain IDs:B
Chain Length:221
Number of Molecules:1
Biological Source:Mus musculus, Homo sapiens
Polymer Type:polypeptide(L)
Description:CETUXIMAB FAB HEAVY CHAIN
Chain IDs:D
Chain Length:221
Number of Molecules:1
Biological Source:Mus musculus, Homo sapiens
Polymer Type:polypeptide(L)
Description:CYCLIC MEDITOPE CQA(Ph)2DLSTRRLKC
Chain IDs:E, F
Chain Length:12
Number of Molecules:2
Biological Source:synthetic construct
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2GX E PHE BETA-PHENYL-L-PHENYLALANINE
ASN B ASN GLYCOSYLATION SITE
PCA B GLN PYROGLUTAMIC ACID
Primary Citation
Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.
Acta Crystallogr F Struct Biol Commun 72 820 830 (2016)
PMID: 27834791 DOI: 10.1107/S2053230X16016149

Abstact

Herein, multiple crystal structures of meditope peptide derivatives incorporating natural and unnatural amino acids bound to the cetuximab Fab domain are presented. The affinity of each derivative was determined by surface plasmon resonance and correlated to the atomic structure. Overall, it was observed that the hydrophobic residues in the meditope peptide, Phe3, Leu5 and Leu10, could accommodate a number of moderate substitutions, but these invariably reduced the overall affinity and half-life of the interaction. In one case, the substitution of Phe3 by histidine led to a change in the rotamer conformation, in which the imidazole ring flipped to a solvent-exposed position. Based on this observation, Phe3 was substituted by diphenylalanine and it was found that the phenyl rings in this variant mimic the superposition of the Phe3 and His3 structures, producing a moderate increase, of 1.4-fold, in the half-life of the complex. In addition, it was observed that substitution of Leu5 by tyrosine and glutamate strongly reduced the affinity, whereas the substitution of Leu5 by diphenylalanine moderately reduced the half-life (by approximately fivefold). Finally, it was observed that substitution of Arg8 and Arg9 by citrulline dramatically reduced the overall affinity, presumably owing to lost electrostatic interactions. Taken together, these studies provide insight into the meditope-cetuximab interaction at the atomic level.

Legend

Protein

Chemical

Disease

Primary Citation of related structures