3L9J Immune System date Jan 05, 2010
title Selection Of A Novel Highly Specific Tnfalpha Antagonist: In The Crystal Structure Of The Antagonist-Tnfalpha Complex
authors P.Byla, M.H.Andersen, H.C.Thogersen, H.H.Gad, R.Hartmann
compound source
Molecule: Tnfalpha
Chain: C
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pt7ciih6

Molecule: Tumor Necrosis Factor, Soluble Form
Chain: T
Fragment: Unp Residues 85-233
Synonym: Tnf-Alpha, Tumor Necrosis Factor Ligand Superfamil 2, Tnf-A, Cachectin;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pt7ciih6
symmetry Space Group: P 63 2 2
R_factor 0.173 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.905 83.905 149.172 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand MG enzyme
Primary referenceSelection of a novel and highly specific tumor necrosis factor alpha (TNFalpha) antagonist: insight from the crystal structure of the antagonist-TNFalpha complex., Byla P, Andersen MH, Holtet TL, Jacobsen H, Munch M, Gad HH, Thogersen HC, Hartmann R, J Biol Chem. 2010 Apr 16;285(16):12096-100. Epub 2010 Feb 23. PMID:20179326
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (3l9j.pdb1.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 3L9J
  • CSU: Contacts of Structural Units for 3L9J
  • Structure Factors (254 Kb)
  • Retrieve 3L9J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L9J from S2C, [Save to disk]
  • Re-refined 3l9j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3L9J 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 3L9J
  • 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 3L9J, from MSDmotif at EBI
  • Fold representative 3l9j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l9j] [3l9j_C] [3l9j_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3L9J: [CLECT] [TNF ] by SMART
  • Other resources with information on 3L9J
  • Community annotation for 3L9J 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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