2ZJC Cytokine date Mar 05, 2008
title Tnfr1 Selectve Tnf Mutant; R1-6
authors Y.Mukai, Y.Yamagata, Y.Tsutsumi
compound source
Molecule: Tumor Necrosis Factor
Chain: A, B, C
Fragment: R1-6, Unp Residues 77-233
Synonym: Tnf-Alpha, Tumor Necrosis Factor Ligand Superfamil 2, Tnf-A, Cachectin;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnf, Tnfa, Tnfsf2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pyas(Modifed From Puc Vector)
symmetry Space Group: H 3
R_factor 0.201 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.873 135.873 58.023 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand GOL enzyme
Primary referenceStructure-Function Relationship of Tumor Necrosis Factor (TNF) and Its Receptor Interaction Based on 3D Structural Analysis of a Fully Active TNFR1-Selective TNF Mutant., Mukai Y, Shibata H, Nakamura T, Yoshioka Y, Abe Y, Nomura T, Taniai M, Ohta T, Ikemizu S, Nakagawa S, Tsunoda SI, Kamada H, Yamagata Y, Tsutsumi Y, J Mol Biol. 2009 Jan 30;385(4):1221-1229. Epub 2008 Dec 6. PMID:19084540
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (2zjc.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 2ZJC
  • CSU: Contacts of Structural Units for 2ZJC
  • Likely Quarternary Molecular Structure file(s) for 2ZJC
  • Structure Factors (118 Kb)
  • Retrieve 2ZJC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZJC from S2C, [Save to disk]
  • Re-refined 2zjc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZJC 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 2ZJC
  • 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 2ZJC, from MSDmotif at EBI
  • Fold representative 2zjc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zjc_C] [2zjc_A] [2zjc_B] [2zjc]
  • SWISS-PROT database: [P01375]
  • Domain organization of [TNFA_HUMAN] by SWISSPFAM
  • Domain found in 2ZJC: [TNF ] by SMART
  • Alignments of the sequence of 2ZJC with the sequences similar proteins can be viewed for 2ZJC's classification [TNFA_HUMAN] 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 [TNFA_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2ZJC
  • Community annotation for 2ZJC 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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