3FXI Immune System date Jan 21, 2009
title Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps Ra
authors B.S.Park, D.H.Song, H.M.Kim, J.O.Lee
compound source
Molecule: Toll-Like Receptor 4
Chain: A, B
Fragment: Extracellular Domain, Residues 27-631
Synonym: Tlr4, Htoll
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tlr4
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_cell: High Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pacgp67a

Molecule: Lymphocyte Antigen 96
Chain: C, D
Synonym: Md-2, Protein Md-2, Esop-1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Esop1, Ly96, Md-2, Md2
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_cell: High Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pacgp67a
symmetry Space Group: P 21 21 21
R_factor 0.241 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.160 103.500 251.810 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand DAO, FTT, GCS, GMH, KDO, MG, MYR, NAG, PA1, PO4 enzyme
note 3FXI (Molecule of the Month:pdb143)
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceThe structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex., Park BS, Song DH, Kim HM, Choi BS, Lee H, Lee JO, Nature. 2009 Apr 30;458(7242):1191-5. Epub 2009 Mar 1. PMID:19252480
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (257 Kb) [Save to disk]
  • Biological Unit Coordinates (3fxi.pdb1.gz) 247 Kb
  • LPC: Ligand-Protein Contacts for 3FXI
  • CSU: Contacts of Structural Units for 3FXI
  • Likely Quarternary Molecular Structure file(s) for 3FXI
  • Structure Factors (371 Kb)
  • Retrieve 3FXI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FXI from S2C, [Save to disk]
  • Re-refined 3fxi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FXI 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 3FXI
  • 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 3FXI, from MSDmotif at EBI
  • Fold representative 3fxi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fxi_C] [3fxi] [3fxi_D] [3fxi_B] [3fxi_A]
  • SWISS-PROT database: [Q9Y6Y9] [O00206]
  • Belongs to the neat-domain containing methaemoglobin heme sequestration (n-mhs) family according to TCDB.
  • Domain organization of [LY96_HUMAN] [TLR4_HUMAN] by SWISSPFAM
  • Domains found in 3FXI: [LRR] [LRRCT] [LRR_TYP] [ML ] by SMART
  • Other resources with information on 3FXI
  • Community annotation for 3FXI at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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