1R6D	Lyase	date	Oct 14, 2003
title	Crystal Structure Of Desiv Double Mutant (Dtdp-Glucose 4,6- Dehydratase) From Streptomyces Venezuelae With Nad And Dau
authors	S.T.M.Allard, W.W.Cleland, H.M.Holden
compound		source
Molecule: Tdp-Glucose-4,6-Dehydratase Chain: A Synonym: Dtdp-Glucose 4,6-Dehydratase Ec: 4.2.1.46 Engineered: Yes Mutation: Yes		Organism_scientific: Streptomyces Venezuelae Organism_taxid: 54571 Gene: Desiv Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta(De3)Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-28
symmetry	Space Group: P 21 21 2	R_factor 0.174 R_Free 0.216
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.700 99.400 42.200 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.35 Å
ligand	DAU, NAD	enzyme	Lyase E.C.4.2.1.46 BRENDA
note	1R6D is a representative structure
related structures	by homologous chain: 1R66
Gene Ontology	Chain Function Process Component A oxidoreductase activity
Primary reference	High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae., Allard ST, Cleland WW, Holden HM, J Biol Chem 2004 Jan 16;279(3):2211-20. Epub 2003 Oct 21. PMID:14570895

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (64 Kb) [Save to disk] Biological Unit Coordinates (1r6d.pdb1.gz) 116 Kb LPC: Ligand-Protein Contacts for 1R6D CSU: Contacts of Structural Units for 1R6D Likely Quarternary Molecular Structure file(s) for 1R6D Structure Factors (600 Kb) Retrieve 1R6D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1R6D from S2C, [Save to disk] Re-refined 1r6d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1R6D 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 1R6D

Ramachandran plot from PDBSum

Structure-derived information

Conformational Epitope Prediction for 1R6D 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 1R6D, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1r6da_, region A [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1r6d] [1r6d_A] SWISS-PROT database: [Q9ZGH3] Domain organization of [Q9ZGH3_9ACTO] by SWISSPFAM

Other resources with information on 1R6D

Community annotation for 1R6D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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