› 3ula

X-ray diffraction
3.6Å resolution

Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex

Released:
DOI: 10.2210/pdb3ula/pdb
PDB entry 3ula coloured by chain, front view.
PDB entry 3ula coloured by chain, side view.
PDB entry 3ula coloured by chain, top view.
Source organisms:
Primary publication:
Structure-based rational design of a Toll-like receptor 4 (TLR4) decoy receptor with high binding affinity for a target protein.
Han J, Kim HJ, Lee SC, Hong S, Park K, Jeon YH, Kim D, Cheong HK, Kim HS
PLoS One 7 e30929 (2012)
PMID: 22363519

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126151 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
LRRNT domain-containing protein; Toll-like receptor 4 Chains: A, C
Molecule details ›
Chains: A, C
Length: 279 amino acids
Theoretical weight: 31.43 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O00206 (Residues: 27-228; Coverage: 25%)
  • Canonical: Q4G1L2 (Residues: 126-199; Coverage: 30%)
Gene names: TLR4, VLRB
Sequence domains:
Structure domains: Ribonuclease Inhibitor
Lymphocyte antigen 96 Chains: B, D
Molecule details ›
Chains: B, D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9Y6Y9 (Residues: 19-158; Coverage: 99%)
Gene names: ESOP1, LY96, MD2
Sequence domains: ML domain
Structure domains: Immunoglobulin-like

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
2 bound ligands:
Ligand NAG 4 x NAG
Ligand E55 2 x E55
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P212121
Unit cell:
a: 80.21Å b: 126.935Å c: 129.506Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.306 0.306 0.341
Expression system: Spodoptera frugiperda

Quick links

Citations

5 review citations

TLR4 Signaling Pathway Modulators as Potential Therapeutics in Inflammation and Sepsis.
Kuzmich et al. (2017)
4 more

4 mentions without citation

TLR4-Targeting Therapeutics: Structural Basis and Computer-Aided Drug Discovery Approaches.
Ain et al. (2020)
3 more