4KG8 Cytokine date Apr 28, 2013
title Crystal Structure Of Light Mutant
authors W.Liu, C.Zhan, P.R.Kumar, J.B.Bonanno, S.G.Nathenson, S.C.Almo, Ne Structural Genomics Research Consortium (Nysgrc), Atoms-To-A The Immune Function Network (Ifn)
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1
Chain: A, B, C
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_vector_type: Plasmid
Expression_system_plasmid: Pet3a
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.286
length a length b length c angle alpha angle beta angle gamma
59.644 46.911 70.400 90.00 98.02 90.00
method X-Ray Diffractionresolution 2.25 Å
A, C, 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] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (4kg8.pdb1.gz) 59 Kb
  • CSU: Contacts of Structural Units for 4KG8
  • Structure Factors (395 Kb)
  • Retrieve 4KG8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KG8 from S2C, [Save to disk]
  • Re-refined 4kg8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KG8 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 4KG8
  • 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 4KG8, from MSDmotif at EBI
  • Fold representative 4kg8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kg8] [4kg8_A] [4kg8_B] [4kg8_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4KG8: [TNF ] by SMART
  • Other resources with information on 4KG8
  • Community annotation for 4KG8 at PDBWiki (http://pdbwiki.org)

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