4KGG Crystal structure of light mutant2 and dcr3 complex date 2013-04-29
authors Liu, W., Bonanno, J.B., Zhan, C., Kumar, P.R., Toro, R., Nathenson, S.G., Almo, S.C., IFN, Atoms-to-Animals:.The.Immune.Function.Network., NYSGRC, New.York.Structural.Genomics.Research.Consortium.
compound source
symmetry
R_factor
R_Free 0.23466
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.78
ligand BMA, MAN, MG, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceMechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly., Liu W, Zhan C, Cheng H, Kumar PR, Bonanno JB, Nathenson SG, Almo SC, Structure. 2014 Sep 2;22(9):1252-62. doi: 10.1016/j.str.2014.06.013. Epub 2014, Jul 31. PMID:25087510
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (4kgg.pdb1.gz) 284 Kb
  • Biological Unit Coordinates (4kgg.pdb2.gz) 145 Kb
  • Biological Unit Coordinates (4kgg.pdb3.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 4KGG
  • CSU: Contacts of Structural Units for 4KGG
  • Structure Factors (613 Kb)
  • Retrieve 4KGG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KGG from S2C, [Save to disk]
  • Re-refined 4kgg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KGG 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 4KGG
  • 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 4KGG, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kgg_D] [4kgg_C] [4kgg] [4kgg_B] [4kgg_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KGG: [TNF] [TNFR ] by SMART
  • Other resources with information on 4KGG
  • Community annotation for 4KGG at PDBWiki (http://pdbwiki.org)

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