3ULA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.341
  • R-Value Work: 0.306

Literature

Macromolecules
Sequence Display for 3ULA

Classification: IMMUNE SYSTEM

Total Structure Weight: 100267.05

Macromolecule Entities
Molecule Chains Length Organism Details
Toll-like receptor 4, Variable lymphocyte receptor B A, C 279 Eptatretus burgeri Homo sapiens Fragment: UNP RESIDUES 27-228, UNP RESIDUES 126-199
Mutation: F63W
Details: THE FUSION PROTEIN OF TLR4 (UNP RESIDUES 27-228) AND VLRB (UNP RESIDUES 126-199)
Gene Name(s): TLR4 Gene View VLRB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Lymphocyte antigen 96 B, D 142 Homo sapiens Fragment: UNP RESIDUES 19-158
Mutation: R56G
Gene Name(s): LY96 Gene View ESOP1 MD2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
E55
Query on E55

A, C 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)- 3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC- 11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}- 2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO- ALPHA-D-GLUCOPYRANOSE
E5564, ERITORAN (Synonym)
C66 H126 N2 O19 P2
BPSMYQFMCXXNPC-MFCPCZTFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, C N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, C BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
E55 IC50: 1.5 nM (97) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.341
  • R-Value Work: 0.306
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 80.21 α = 90.00
b = 126.93 β = 90.00
c = 129.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-11-10
  • Released Date: 2012-04-04
  • Deposition author(s): Kim, H.J., Cheong, H.K., Jeon, Y.H.

Revision History

  • 2013-10-09
    Type: Derived calculations
  • 2017-08-23
    Type: Advisory, Refinement description, Source and taxonomy