2AZ5 Cytokine date Sep 09, 2005
title Crystal Structure Of Tnf-Alpha With A Small Molecule Inhibitor
authors M.M.He
compound source
Molecule: Tumor Necrosis Factor (Tnf-Alpha) (Tumor Necrosis Factor Ligand Superfamily Member 2) (Tnf-A)
(Cachectin) [Contains: Tumor Necrosis Factor, Membrane Form; Tumor Necrosis Factor, Soluble Form];
Chain: A, B, C, D
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnf, Tnfa, Tnfsf2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prset
symmetry Space Group: H 3
R_factor 0.220 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
165.254 165.254 63.728 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand 307 BindingDB enzyme
Primary referenceSmall-molecule inhibition of TNF-alpha., He MM, Smith AS, Oslob JD, Flanagan WM, Braisted AC, Whitty A, Cancilla MT, Wang J, Lugovskoy AA, Yoburn JC, Fung AD, Farrington G, Eldredge JK, Day ES, Cruz LA, Cachero TG, Miller SK, Friedman JE, Choong IC, Cunningham BC, Science 2005 Nov 11;310(5750):1022-5. PMID:16284179
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (2az5.pdb1.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 2AZ5
  • CSU: Contacts of Structural Units for 2AZ5
  • Likely Quarternary Molecular Structure file(s) for 2AZ5
  • Structure Factors (417 Kb)
  • Retrieve 2AZ5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2AZ5 from S2C, [Save to disk]
  • Re-refined 2az5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2AZ5 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 2AZ5
  • 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 2AZ5, from MSDmotif at EBI
  • Fold representative 2az5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2az5_D] [2az5_C] [2az5_B] [2az5_A] [2az5]
  • SWISS-PROT database: [P01375]
  • Domain organization of [TNFA_HUMAN] by SWISSPFAM
  • Domain found in 2AZ5: [TNF ] by SMART
  • Alignments of the sequence of 2AZ5 with the sequences similar proteins can be viewed for 2AZ5'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 2AZ5
  • Community annotation for 2AZ5 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science