1A8M Lymphokine date Mar 27, 1998
title Tumor Necrosis Factor Alpha, R31d Mutant
authors C.Reed, Z.Q.Fu, J.Wu, Y.N.Xue, R.W.Harrison, M.J.Chen, I.T.Weber
compound source
Molecule: Tumor Necrosis Factor Alpha
Chain: A, B, C
Synonym: Tnf-Alpha
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41 21 2
R_factor 0.218 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.700 94.700 117.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
related structures by homologous chain: 4TSV, 5TSW
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceCrystal structure of TNF-alpha mutant R31D with greater affinity for receptor R1 compared with R2., Reed C, Fu ZQ, Wu J, Xue YN, Harrison RW, Chen MJ, Weber IT, Protein Eng 1997 Oct;10(10):1101-7. PMID:9488135
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (1a8m.pdb1.gz) 74 Kb
  • CSU: Contacts of Structural Units for 1A8M
  • Likely Quarternary Molecular Structure file(s) for 1A8M
  • Structure Factors (150 Kb)
  • Retrieve 1A8M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1A8M from S2C, [Save to disk]
  • Re-refined 1a8m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1A8M 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 1A8M
  • VIPERdb: visual, structural and computational analysis of 1A8M
  • 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 1A8M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1a8ma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1a8mb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1a8mc_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1a8m 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: [1a8m_A] [1a8m_C] [1a8m] [1a8m_B]
  • SWISS-PROT database: [P01375]
  • Domain organization of [TNFA_HUMAN] by SWISSPFAM
  • Domain found in 1A8M: [TNF ] by SMART
  • Alignments of the sequence of 1A8M with the sequences similar proteins can be viewed for 1A8M'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 1A8M
  • Community annotation for 1A8M 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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