2Z65 Immune System date Jul 22, 2007
title Crystal Structure Of The Human Tlr4 Tv3 Hybrid-Md-2-Eritoran
authors J.O.Lee, H.M.Kim, B.S.Park
compound source
Molecule: Toll-Like Receptor 4, Variable Lymphocyte Recepto
Chain: A, B
Fragment: Tv3, Unp Residues 27-228(Human), E5564, Unp Resid 158(Inshore Hagfish);
Synonym: Htoll, Cd284 Antigen(Human)
Engineered: Yes
Organism_scientific: Homo Sapiens, Eptatretus Burgeri
Organism_common: Human, Inshore Hagfish
Organism_taxid: 9606, 7764
Gene: Tlr4, Vlrb.61
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Hi-5
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pvl1393

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Md-2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Hi-5
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pvl1393
symmetry Space Group: P 1 21 1
R_factor 0.238 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.192 80.987 107.762 90.00 93.01 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand BMA, E55, NAG, NDG BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceCrystal Structure of the TLR4-MD-2 Complex with Bound Endotoxin Antagonist Eritoran., Kim HM, Park BS, Kim JI, Kim SE, Lee J, Oh SC, Enkhbayar P, Matsushima N, Lee H, Yoo OJ, Lee JO, Cell. 2007 Sep 7;130(5):906-17. PMID:17803912
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (2z65.pdb1.gz) 48 Kb
  • Biological Unit Coordinates (2z65.pdb2.gz) 48 Kb
  • Biological Unit Coordinates (2z65.pdb3.gz) 28 Kb
  • Biological Unit Coordinates (2z65.pdb4.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 2Z65
  • CSU: Contacts of Structural Units for 2Z65
  • Likely Quarternary Molecular Structure file(s) for 2Z65
  • Structure Factors (850 Kb)
  • Retrieve 2Z65 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Z65 from S2C, [Save to disk]
  • Re-refined 2z65 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Z65 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 2Z65
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2Z65, from MSDmotif at EBI
  • Fold representative 2z65 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2z65_D] [2z65_C] [2z65_B] [2z65_A] [2z65]
  • 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 2Z65: [LRR] [LRRCT] [LRR_TYP] [ML ] by SMART
  • Other resources with information on 2Z65
  • Community annotation for 2Z65 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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