3ULA Immune System date Nov 10, 2011
title Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran Compl
authors H.J.Kim, H.K.Cheong, Y.H.Jeon
compound source
Molecule: Toll-Like Receptor 4, Variable Lymphocyte Recepto
Chain: A, C
Fragment: Unp Residues 27-228, Unp Residues 126-199
Synonym: Htoll
Engineered: Yes
Mutation: Yes
Other_details: The Fusion Protein Of Tlr4 (Unp Residues 27- Vlrb (Unp Residues 126-199);
Organism_scientific: Homo Sapiens, Eptatretus Burgeri
Organism_common: Human, Inshore Hagfish
Organism_taxid: 9606, 7764
Gene: Tlr4, Vlrb
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Lymphocyte Antigen 96
Chain: B, D
Fragment: Unp Residues 19-158
Synonym: Ly-96, Esop-1, Protein Md-2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ly96, Esop1, Md2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 21 21 21
R_factor 0.306 R_Free 0.341
length a length b length c angle alpha angle beta angle gamma
80.210 126.935 129.506 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand BMA, E55, NAG BindingDB enzyme
A, C

D, B

Primary referenceStructure-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. 2012;7(2):e30929. Epub 2012 Feb 17. PMID:22363519
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (3ula.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (3ula.pdb2.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 3ULA
  • CSU: Contacts of Structural Units for 3ULA
  • Structure Factors (849 Kb)
  • Retrieve 3ULA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ULA from S2C, [Save to disk]
  • Re-refined 3ula structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ULA in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3ULA
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3ULA, from MSDmotif at EBI
  • Fold representative 3ula from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ula] [3ula_C] [3ula_B] [3ula_A] [3ula_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3ULA: [LRR] [LRRCT] [LRR_TYP] [ML ] by SMART
  • Other resources with information on 3ULA
  • Community annotation for 3ULA at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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