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
Gene
Ontology
ChainFunctionProcessComponent
C


T


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
  • Alignments of the sequence of 3L9J with the sequences similar proteins can be viewed for 3L9J's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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