2TNF Cytokine date Oct 12, 1998
title 1.4 A Resolution Structure Of Mouse Tumor Necrosis Factor, T Modulation Of Its Selectivity And Trimerisation
authors K.J.Baeyens, H.L.De Bondt, A.Raeymaekers, W.Fiers, C.J.De Ranter
compound source
Molecule: Protein (Tumor Necrosis Factor Alpha)
Chain: A, B, C
Fragment: Residues 80-235
Synonym: Tnf-Alpha, Cachectin
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.201 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.214 48.300 51.095 114.81 103.65 91.05
method X-Ray Diffractionresolution 1.40 Å
ligand IPA, TRS enzyme
note 2TNF is a representative structure
related structures by homologous chain: 1KMJ, 4TSV
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceThe structure of mouse tumour-necrosis factor at 1.4 A resolution: towards modulation of its selectivity and trimerization., Baeyens KJ, De Bondt HL, Raeymaekers A, Fiers W, De Ranter CJ, Acta Crystallogr D Biol Crystallogr 1999 Apr;55 ( Pt 4):772-8. PMID:10089307
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2tnf.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 2TNF
  • CSU: Contacts of Structural Units for 2TNF
  • Likely Quarternary Molecular Structure file(s) for 2TNF
  • Structure Factors (626 Kb)
  • Retrieve 2TNF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2TNF from S2C, [Save to disk]
  • Re-refined 2tnf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2TNF 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 2TNF
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 2TNF 2TNFA 2TNFB 2TNFC from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2TNF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2tnfa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d2tnfb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d2tnfc_, region C [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2tnf_A] [2tnf] [2tnf_C] [2tnf_B]
  • SWISS-PROT database: [P06804]
  • Domain organization of [TNFA_MOUSE] by SWISSPFAM
  • Domain found in 2TNF: [TNF ] by SMART
    • Other resources with information on 2TNF
  • Community annotation for 2TNF 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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