4KGG Cytokine Signaling Protein date Apr 29, 2013
title Crystal Structure Of Light Mutant2 And Dcr3 Complex
authors W.Liu, J.B.Bonanno, C.Zhan, P.R.Kumar, R.Toro, S.G.Nathenson, S.C. Atoms-To-Animals: The Immune Function Network (Ifn), New Yor Structural Genomics Research Consortium (Nysgrc)
compound source
Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: C, D
Fragment: 30-195
Synonym: Decoy Receptor 3, Dcr3, Decoy Receptor For Fas Lig
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfrsf6b, Dcr3, Tr6, Unq186pro212
Expression_system: Drosophila
Expression_system_taxid: 7215
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmt-Bip-His-V5

Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1
Chain: A, B
Fragment: 83-240
Synonym: Herpes Virus Entry Mediator Ligand, Hvem-L, Herpes Entry Mediator Ligand, Tumor Necrosis Factor Ligand Superfa Member 14, Membrane Form, Tumor Necrosis Factor Ligand Supe Member 14, Soluble Form;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfsf14, Hveml, Light, Unq391pro726
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Phys
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a
symmetry Space Group: P 21 3
R_factor 0.178 R_Free 0.235
length a length b length c angle alpha angle beta angle gamma
148.754 148.754 148.754 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.78 Å
ligand BMA, MAN, MG, NAG enzyme
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
  • 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 4KGG, from MSDmotif at EBI
  • Fold representative 4kgg from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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