› 3ul8

X-ray diffraction
2.5Å resolution

Crystal structure of the TV3 mutant V134L

Released:
DOI: 10.2210/pdb3ul8/pdb
Model geometry
Fit model/data
PDB entry 3ul8 coloured by chain, front view.
PDB entry 3ul8 coloured by chain, side view.
PDB entry 3ul8 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
OpenAccess logo PLoS One 7 e30929 (2012)
PMID: 22363519

Function and Biology Details

Reaction catalysed: 
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126150 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
LRRNT domain-containing protein; Toll-like receptor 4 Chain: A
Molecule details ›
Chain: A
Length: 279 amino acids
Theoretical weight: 31.4 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

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
3 bound ligands:
Ligand NAG 1 x NAG
Ligand FUL 1 x FUL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P212121
Unit cell:
a: 32.04Å b: 50.5Å c: 192.78Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.24 0.24 0.3
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

2 mentions without citation

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

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO