5YY4 image
Entry Detail
PDB ID:
5YY4
Keywords:
Title:
Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2017-12-07
Release Date:
2018-07-18
Method Details:
Experimental Method:
Resolution:
1.59 Å
R-Value Free:
0.19
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:scFv 4B08
Chain IDs:A
Chain Length:252
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:C-C chemokine receptor type 5
Chain IDs:B
Chain Length:9
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
TYS B TYR modified residue
Primary Citation
Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody
Biochemistry 57 4177 4185 (2018)
PMID: 29936828 DOI: 10.1021/acs.biochem.8b00592

Abstact

Protein tyrosine sulfation (PTS) is a post-translational modification regulating numerous biological events. PTS generally occurs at flexible regions of proteins, enhancing intermolecular interactions between proteins. Because of the high flexibility associated with the regions where PTS is generally encountered, an atomic-level understanding has been difficult to achieve by X-ray crystallography or nuclear magnetic resonance techniques. In this study, we focused on the conformational behavior of a flexible sulfated peptide and its interaction with an antibody. Molecular dynamics simulations and thermodynamic analysis indicated that PTS reduced the main-chain fluctuations upon the appearance of sulfate-mediated intramolecular H-bonds. Collectively, our data suggested that one of the mechanisms by which PTS may enhance protein-protein interactions consists of the limitation of conformational dynamics in the unbound state, thus reducing the loss of entropy upon binding and boosting the affinity for its partner.

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