1DG6 Apoptosis date Nov 23, 1999
title Crystal Structure Of Apo2ltrail
authors S.G.Hymowitz, M.P.O'Connell, M.H.Ultsch, A.M.De Vos, R.F.Kelley
compound source
Molecule: Apo2ltnf-Related Apopotis Inducing Ligand (Trail
Chain: A
Fragment: Trimeric Jelly-Roll Domain Of Apo2l
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Human Placenta
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Trp Promoter
Other_details: Human Placenta
symmetry Space Group: H 3 2
length a length b length c angle alpha angle beta angle gamma
66.435 66.435 197.727 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.30 Å
ligand CL, ZN enzyme
note 1DG6 is a representative structure
related structures by homologous chain: 1D4V

Primary referenceA unique zinc-binding site revealed by a high-resolution X-ray structure of homotrimeric Apo2L/TRAIL., Hymowitz SG, O'Connell MP, Ultsch MH, Hurst A, Totpal K, Ashkenazi A, de Vos AM, Kelley RF, Biochemistry 2000 Feb 1;39(4):633-40. PMID:10651627
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (1dg6.pdb1.gz) 90 Kb
  • LPC: Ligand-Protein Contacts for 1DG6
  • CSU: Contacts of Structural Units for 1DG6
  • Likely Quarternary Molecular Structure file(s) for 1DG6
  • Structure Factors (411 Kb)
  • Retrieve 1DG6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DG6 from S2C, [Save to disk]
  • Re-refined 1dg6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DG6 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 1DG6
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1DG6 from the CEP Server.
  • 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 1DG6, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dg6a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1dg6 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: [1dg6_A] [1dg6]
  • SWISS-PROT database: [P50591]
  • Domain organization of [TNF10_HUMAN] by SWISSPFAM
  • Domain found in 1DG6: [TNF ] by SMART
  • Other resources with information on 1DG6
  • Community annotation for 1DG6 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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