1Q3F

Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA

Structural Biology Knowledgebase: 1Q3F SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 1Q3F

Classification: HYDROLASE / DNA

Total Structure Weight: 31408.26


Macromolecule Entities
Molecule Chains Length Organism Details
Uracil-DNA glycosylase A 223 Homo sapiens EC#: 3.2.2.27 IUBMB
Gene Name(s): UNG Gene View DGU UNG1 UNG15
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*TP*GP*TP*(NRI)P*AP*TP*CP*TP*T)-3' B 9 synthetic 1-aza-2'-deoxyribose-containing DNA
5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3' C 10 synthetic

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

B URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
NRI
Query on NRI
B DNA LINKING C5 H12 N O5 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.190
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 48.64 α = 90.00
b = 65.89 β = 90.00
c = 99.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-07-29
  • Released Date: 2004-03-23
  • Deposition author(s): Bianchet, M.A., Seiple, L.A., Jiang, Y.L., Ichikawa, Y., Amzel, L.M., Stivers, J.T.

Revision History

  • 2015-10-07
    Type: Entry title | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4