5IJC	Immune System	date	Mar 01, 2016
title	The Crystal Structure Of Mouse Tlr4md-2neoseptin-3 Complex
authors	Y.Wang, L.Su, M.D.Morin, B.T.Jones, L.R.Whitby, M.Surakattula, H.H H.Shi, J.H.Choi, K.Wang, E.M.Moresco, M.Berger, X.Zhan, H.Zhang, D B.Beutler
compound		source
Molecule: Toll-Like Receptor 4,Variable Lymphocyte Receptor Chain: A, B Fragment: Tlr4 Ectodomain (Unp Residues 26-544) + Vlrb (Unp 126-200); Ec: 3.2.2.6 Engineered: Yes		Organism_scientific: Mus Musculus, Eptatretus Burgeri Organism_common: Mouse, Inshore Hagfish Organism_taxid: 10090, 7764 Gene: Tlr4, Lps, Vlrb Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108
Molecule: Lymphocyte Antigen 96 Chain: C, D Fragment: Unp Residues 19-160 Synonym: Ly-96,Esop-1,Protein Md-2 Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Gene: Ly96, Esop1, Md2 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108
symmetry	Space Group: P 1 21 1	R_factor 0.193 R_Free 0.234
crystal cell	length a length b length c angle alpha angle beta angle gamma 70.752 148.559 131.720 90.00 98.30 90.00
method	X-Ray Diffraction	resolution	2.57 Å
ligand	NAG, V2A	enzyme	Hydrolase E.C.3.2.2.6 BRENDA
note	5IJC supersedes 5HG4
Gene Ontology	Chain Function Process Component A, B D, C
Primary reference	TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS., Wang Y, Su L, Morin MD, Jones BT, Whitby LR, Surakattula MM, Huang H, Shi H, Choi JH, Wang KW, Moresco EM, Berger M, Zhan X, Zhang H, Boger DL, Beutler B, Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):E884-93. doi:, 10.1073/pnas.1525639113. Epub 2016 Feb 1. PMID:26831104

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (505 Kb) [Save to disk] Biological Unit Coordinates (5ijc.pdb1.gz) 247 Kb Biological Unit Coordinates (5ijc.pdb2.gz) 248 Kb LPC: Ligand-Protein Contacts for 5IJC CSU: Contacts of Structural Units for 5IJC Structure Factors (1683 Kb) Retrieve 5IJC in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5IJC from S2C, [Save to disk] Re-refined 5ijc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5IJC 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 5IJC

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5ijc_D] [5ijc_A] [5ijc_C] [5ijc] [5ijc_B] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5IJC: [LRR] [LRRCT] [LRR_TYP] [ML ] by SMART

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