1Y6F Transferase Dna date Dec 06, 2004
title Alpha-Glucosyltransferase In Complex With Udp-Glucose And Dn Containing An Abasic Site
authors L.Lariviere, N.Sommer, S.Morera
compound source
Molecule: 5'-D(Gpaptpapcptp(3dr)Papgpaptpapg)-
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Cptpaptpcptpgpapgptpaptpc)-3'
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Dna Alpha-Glucosyltransferase
Chain: A, B
Synonym: Agt
Ec: 2.4.1.26
Engineered: Yes

Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Xl1blue
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Proexhtb
symmetry Space Group: P 1 21 1
R_factor 0.197 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.363 123.964 86.628 90.00 101.83 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 3DR, GOL, PEG, UDP, UPG enzyme Transferase E.C.2.4.1.26 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural Evidence of a Passive Base-flipping Mechanism for AGT, an Unusual GT-B Glycosyltransferase., Lariviere L, Sommer N, Morera S, J Mol Biol 2005 Sep 9;352(1):139-50. PMID:16081100
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (152 Kb) [Save to disk]
  • Biological Unit Coordinates (1y6f.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (1y6f.pdb2.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 1Y6F
  • CSU: Contacts of Structural Units for 1Y6F
  • Likely Quarternary Molecular Structure file(s) for 1Y6F
  • Structure Factors (306 Kb)
  • Retrieve 1Y6F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y6F from S2C, [Save to disk]
  • Re-refined 1y6f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y6F 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 1Y6F
  • 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
  • 3D motif for 1Y6F, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y6f] [1y6f_C] [1y6f_D] [1y6f_B] [1y6f_A]
  • SWISS-PROT database: [P04519]
  • Domain organization of [GSTA_BPT4] by SWISSPFAM
  • Other resources with information on 1Y6F
  • Community annotation for 1Y6F 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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