3CXM

Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Leishmania naiffi uracil-DNA glycosylase in complex with several ligands identified with fragment cocktail crystallography.

Larson, E.T.Merritt, E.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
A
268Leishmania naiffiMutation(s): 0 
EC: 3.2.2.27
Find proteins for D0VWU0 (Leishmania naiffi)
Go to UniProtKB:  D0VWU0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
URB
Query on URB

Download SDF File 
Download CCD File 
A
5-bromopyrimidine-2,4(1H,3H)-dione
5-bromouracil
C4 H3 Br N2 O2
LQLQRFGHAALLLE-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
URA
Query on URA

Download SDF File 
Download CCD File 
A
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.138 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 75.320α = 90.00
b = 75.320β = 90.00
c = 105.703γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description