1Y6G

alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at 2.8 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 1Y6G

Classification: TRANSFERASE / DNA

Total Structure Weight: 103799.46


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*(5HU)P*AP*GP*AP*TP*AP*G)-3' C 13 synthetic
5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*T)-3' D 12 synthetic

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

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

A, B, D COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5HU
Query on 5HU
C DNA LINKING C10 H15 N2 O9 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.219
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 46.99 α = 90.00
b = 120.52 β = 94.68
c = 86.81 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: Version format compliance