› 3ri0

X-ray diffraction
2.25Å resolution

Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins

Released:
DOI: 10.2210/pdb3ri0/pdb
PDB entry 3ri0 coloured by chain, front view.
PDB entry 3ri0 coloured by chain, side view.
PDB entry 3ri0 coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope.
Azoitei ML, Ban YE, Julien JP, Bryson S, Schroeter A, Kalyuzhniy O, Porter JR, Adachi Y, Baker D, Pai EF, Schief WR
J Mol Biol 415 175-92 (2012)
PMID: 22061265

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177886 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 165 amino acids
Theoretical weight: 17.31 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SHN1 (Residues: 2-158; Coverage: 99%)
Gene name: TTHA1699
Sequence domains: Aminoacyl-tRNA editing domain
Structure domains: YbaK/aminoacyl-tRNA synthetase-associated domain

Ligands and Environments

2 bound ligands:
Ligand GOL 1 x GOL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2
Unit cell:
a: 61.6Å b: 80.4Å c: 67.3Å
α: 90° β: 111.9° γ: 90°
R-values:
R R work R free
0.217 0.217 0.236
Expression system: Escherichia coli

Quick links

Citations

24 review citations

Modern subunit vaccines: development, components, and research opportunities.
Moyle et al. (2013)
23 more

2 mentions without citation

Strategies to control the binding mode of de novo designed protein interactions.
Der et al. (2013)
1 more