3LKJ Cytokine date Jan 27, 2010
title Small Molecule Inhibition Of The Tnf Family Cyokine Cd40 Lig Through A Subunit Fracture Mechanism
authors L.F.Silvian, A.Whitty
compound source
Molecule: Cd40 Ligand
Chain: A, B, C
Fragment: Unp Residues 121-261
Synonym: Cd40-L, Tumor Necrosis Factor Ligand Superfamily M Tnf-Related Activation Protein, Trap, T-Cell Antigen Gp39, Ligand, Membrane Form, Cd40 Ligand, Soluble Form;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd40l, Cd40lg, Tnfsf5, Trap
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Yeast
Expression_system_taxid: 4932
symmetry Space Group: P 21 21 21
R_factor 0.226 R_Free 0.305
length a length b length c angle alpha angle beta angle gamma
63.303 67.607 108.534 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand LKJ, NAG enzyme
A, C, B

Primary referenceSmall Molecule Inhibition of the TNF Family Cytokine CD40 Ligand through a Subunit Fracture Mechanism., Silvian LF, Friedman JE, Strauch K, Cachero TG, Day ES, Qian F, Cunningham B, Fung A, Sun L, Su L, Zheng Z, Kumaravel G, Whitty A, ACS Chem Biol. 2011 Jun 17;6(6):636-47. Epub 2011 Apr 20. PMID:21417339
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (3lkj.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 3LKJ
  • CSU: Contacts of Structural Units for 3LKJ
  • Structure Factors (247 Kb)
  • Retrieve 3LKJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LKJ from S2C, [Save to disk]
  • Re-refined 3lkj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LKJ 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 3LKJ
  • 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 3LKJ, from MSDmotif at EBI
  • Fold representative 3lkj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lkj_A] [3lkj_B] [3lkj] [3lkj_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LKJ: [TNF ] by SMART
  • Other resources with information on 3LKJ
  • Community annotation for 3LKJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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