2E7A Cytokine date Jan 09, 2007
title Tnf Receptor Subtype One-Selective Tnf Mutant With Antagonistic Activity
authors Y.Mukai, Y.Yamagata, Y.Tsutsumi
compound source
Molecule: Tumor Necrosis Factor
Chain: A, B, C
Synonym: Tnf
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pyas(Modified From Puc18)
Other_details: This Mutant Was Created By Phage Display System
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.560 66.970 103.560 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
Primary referenceCreation and X-ray structure analysis of the tumor necrosis factor receptor-1-selective mutant of a tumor necrosis factor-alpha antagonist., Shibata H, Yoshioka Y, Ohkawa A, Minowa K, Mukai Y, Abe Y, Taniai M, Nomura T, Kayamuro H, Nabeshi H, Sugita T, Imai S, Nagano K, Yoshikawa T, Fujita T, Nakagawa S, Yamamoto A, Ohta T, Hayakawa T, Mayumi T, Vandenabeele P, Aggarwal BB, Nakamura T, Yamagata Y, Tsunoda S, Kamada H, Tsutsumi Y, J Biol Chem. 2008 Jan 11;283(2):998-1007. Epub 2007 Nov 14. PMID:18003610
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (2e7a.pdb1.gz) 73 Kb
  • CSU: Contacts of Structural Units for 2E7A
  • Likely Quarternary Molecular Structure file(s) for 2E7A
  • Structure Factors (253 Kb)
  • Retrieve 2E7A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2E7A from S2C, [Save to disk]
  • Re-refined 2e7a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2E7A 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 2E7A
  • 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 2E7A, from MSDmotif at EBI
  • Fold representative 2e7a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2e7a] [2e7a_B] [2e7a_C] [2e7a_A]
  • SWISS-PROT database: [P01375]
  • Domain organization of [TNFA_HUMAN] by SWISSPFAM
  • Domain found in 2E7A: [TNF ] by SMART
  • Alignments of the sequence of 2E7A with the sequences similar proteins can be viewed for 2E7A'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 2E7A
  • Community annotation for 2E7A 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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