5TSW Lymphokine date Apr 22, 1999
title High Resolution Crystal Structure Of A Human Tnf-Alpha Mutant
authors S.S.Cha, J.S.Kim, H.S.Cho, B.H.Oh
compound source
Molecule: Protein (Tumor Necrosis Factor-Alpha)
Chain: A, B, C, D, E, F
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)
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.299
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.170 94.560 95.890 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
note 5TSW supersedes 4TSW
related structures by homologous chain: 1A8M, 1TNF
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceHigh resolution crystal structure of a human tumor necrosis factor-alpha mutant with low systemic toxicity., Cha SS, Kim JS, Cho HS, Shin NK, Jeong W, Shin HC, Kim YJ, Hahn JH, Oh BH, J Biol Chem 1998 Jan 23;273(4):2153-60. PMID:9442056
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk]
  • Biological Unit Coordinates (5tsw.pdb1.gz) 91 Kb
  • Biological Unit Coordinates (5tsw.pdb2.gz) 92 Kb
  • CSU: Contacts of Structural Units for 5TSW
  • Likely Quarternary Molecular Structure file(s) for 5TSW
  • Structure Factors (313 Kb)
  • Retrieve 5TSW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TSW from S2C, [Save to disk]
  • Re-refined 5tsw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5TSW 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 5TSW
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 5TSW, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d5tswa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d5tswb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d5tswc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d5tswd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d5tswe_, region E [Jmol] [rasmolscript] [script source]
        - Domain d5tswf_, region F [Jmol] [rasmolscript] [script source]
  • Fold representative 5tsw from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [5tsw_E] [5tsw_D] [5tsw_F] [5tsw_C] [5tsw_B] [5tsw_A] [5tsw]
  • SWISS-PROT database: [P01375]
  • Domain organization of [TNFA_HUMAN] by SWISSPFAM
  • Domain found in 5TSW: [TNF ] by SMART
  • Alignments of the sequence of 5TSW with the sequences similar proteins can be viewed for 5TSW'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 5TSW
  • Community annotation for 5TSW 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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