1Y8Z

alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a HMU base at 1.9 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 1Y8Z

Classification: Transferase / DNA

Total Structure Weight: 102904.04


Macromolecule Entities
Molecule Chains Length Organism Details
DNA alpha-glucosyltransferase A, B 402 Escherichia virus t4 EC#: 2.4.1.26 IUBMB
Mutation: C1014X, C1274X
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*G)-3' D 9 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)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-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 2 Unique
ID Chains Type Formula 2D Diagram Parent
5HU
Query on 5HU
C DNA LINKING C10 H15 N2 O9 P DU
CME
Query on CME
A, B L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.208
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 41.26 α = 90.00
b = 114.65 β = 89.49
c = 86.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-14
  • 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