2ZPX Cytokine date Jul 29, 2008
title Tnf Receptor Subtype One-Selective Tnf Mutant With Antagonistic Activity; R1anttnf-T8
authors Y.Mukai, T.Nakamura, Y.Yamagata, Y.Tsutsumi
compound source
Molecule: Tumor Necrosis Factor
Chain: A, B, C
Fragment: Unp Residues 77-233
Synonym: Tnf-Alpha, Tumor Necrosis Factor Ligand Superfamily Member 2, Tnf-A, Cachectin, Antagonistic Tnf Mutant (R1anttnf-T8);
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Human
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(Modified From Puc18)
symmetry Space Group: P 21 21 21
R_factor 0.268 R_Free 0.309
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.586 111.331 75.382 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.83 Å
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceFast binding kinetics and conserved 3D structure underlie the antagonistic activity of mutant TNF: useful information for designing artificial proteo-antagonists., Mukai Y, Nakamura T, Yoshioka Y, Shibata H, Abe Y, Nomura T, Taniai M, Ohta T, Nakagawa S, Tsunoda S, Kamada H, Yamagata Y, Tsutsumi Y, J Biochem. 2009 Aug;146(2):167-72. Epub 2009 Apr 22. PMID:19386778
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (2zpx.pdb1.gz) 68 Kb
  • CSU: Contacts of Structural Units for 2ZPX
  • Likely Quarternary Molecular Structure file(s) for 2ZPX
  • Structure Factors (78 Kb)
  • Retrieve 2ZPX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZPX from S2C, [Save to disk]
  • Re-refined 2zpx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZPX 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 2ZPX
  • 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 2ZPX, from MSDmotif at EBI
  • Fold representative 2zpx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zpx_B] [2zpx] [2zpx_C] [2zpx_A]
  • SWISS-PROT database: [P01375]
  • Domain organization of [TNFA_HUMAN] by SWISSPFAM
  • Domain found in 2ZPX: [TNF ] by SMART
  • Alignments of the sequence of 2ZPX with the sequences similar proteins can be viewed for 2ZPX'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 2ZPX
  • Community annotation for 2ZPX 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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