1PM5

Crystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 1PM5

Classification: hydrolase / DNA

Total Structure Weight: 39868.41


Macromolecule Entities
Molecule Chains Length Organism Details
Formamidopyrimidine-DNA glycosylase A 271 Lactococcus lactis EC#: 3.2.2.23 IUBMB
Fragment: Fpg
Mutation: ΔD138
Gene Name(s): mutM fpg
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3') D 14 synthetic
DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') E 14 synthetic

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-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
D DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.196
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 91.78 α = 90.00
b = 91.78 β = 90.00
c = 141.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-10
  • Released Date: 2004-07-27
  • Deposition author(s): Pereira de Jesus-Tran, K., Serre, L., Zelwer, C., Castaing, B.

Revision History

  • Version 1_0: 2004-07-27

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance