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	R_factor R_Free
crystal cell	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 Diffraction	resolution	1.30 Å
ligand	CL, ZN	enzyme
note	1DG6 is a representative structure
related structures	by homologous chain: 1D4V
Gene Ontology	Chain Function Process Component A
Primary reference	A 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) 88 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

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 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] 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)

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