1EMJ

URACIL-DNA GLYCOSYLASE BOUND TO DNA CONTAINING A 4'-THIO-2'DEOXYURIDINE ANALOG PRODUCT

Structural Biology Knowledgebase: 1EMJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.228

Literature

Macromolecules
Sequence Display for 1EMJ

Classification: hydrolase / DNA

Total Structure Weight: 31346.33


Macromolecule Entities
Molecule Chains Length Organism Details
URACIL-DNA GLYCOSYLASE A 223 Homo sapiens EC#: 3.2.2.27 IUBMB
Mutation: P82M, V83E, G84F
Details: MITOCHONDRIAL PROTEIN
Gene Name(s): UNG Gene View DGU UNG1 UNG15
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*GP*TP*(ASU)P*AP*TP*CP*TP*T)-3') B 9 synthetic
DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3') C 10 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
URA
Query on URA

A URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ASU
Query on ASU
B DNA LINKING C5 H11 O6 P S --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.228
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 48.55 α = 90.00
b = 64.85 β = 90.00
c = 96.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-03-16
  • Released Date: 2000-05-16
  • Deposition author(s): Parikh, S.S., Walcher, G., Jones, G.D., Slupphaug, G., Krokan, H.E., Blackburn, G.M., Tainer, J.A.

Revision History

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