4G8A Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS date 2012-07-23
authors Ohto, U., Shimizu, T.
compound source
symmetry
R_factor
R_Free 0.24894
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.40
ligand DAO, KDO, LP4, LP5, MYR, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceStructural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I., Ohto U, Yamakawa N, Akashi-Takamura S, Miyake K, Shimizu T, J Biol Chem. 2012 Nov 23;287(48):40611-7. doi: 10.1074/jbc.M112.404608. Epub 2012, Oct 10. PMID:23055527
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (494 Kb) [Save to disk]
  • Biological Unit Coordinates (4g8a.pdb1.gz) 484 Kb
  • LPC: Ligand-Protein Contacts for 4G8A
  • CSU: Contacts of Structural Units for 4G8A
  • Structure Factors (1094 Kb)
  • Retrieve 4G8A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4G8A from S2C, [Save to disk]
  • Re-refined 4g8a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4G8A 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 4G8A
  • 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
  • 3D motif for 4G8A, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4g8a_B] [4g8a_A] [4g8a_C] [4g8a_D] [4g8a]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4G8A: [LRR] [LRRCT] [LRR_TYP] [ML ] by SMART
  • Other resources with information on 4G8A
  • Community annotation for 4G8A at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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