1Y6F

alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 1Y6F

Classification: TRANSFERASE / DNA

Total Structure Weight: 103465.97


Macromolecule Entities
Molecule Chains Length Organism Details
DNA alpha-glucosyltransferase A, B 403 Enterobacteria phage t4 sensu lato EC#: 2.4.1.26 IUBMB
Gene Name(s): agt
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3' C 13 synthetic
5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3' D 13 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UPG
Query on UPG

A URIDINE-5'-DIPHOSPHATE-GLUCOSE
URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER (Synonym)
C15 H24 N2 O17 P2
HSCJRCZFDFQWRP-JZMIEXBBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UDP
Query on UDP

B URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A, B DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
C DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.197
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 47.36 α = 90.00
b = 123.96 β = 101.83
c = 86.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-06
  • Released Date: 2005-08-30
  • Deposition author(s): Lariviere, L., Sommer, N., Morera, S.

Revision History

  • Version 1_0: 2005-08-30

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance