2PY4

Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.170
  • R-Value Work: 0.144

Literature

Macromolecules
Sequence Display for 2PY4

Classification: HYDROLASE

Total Structure Weight: 18605.92

Macromolecule Entities
Molecule Chains Length Organism Details
Deoxyuridine 5'-triphosphate nucleotidohydrolase A 174 Mycobacterium tuberculosis EC#: 3.6.1.23 IUBMB
Gene Name(s): dut Rv2697c MTCY05A6.18c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DUP N/A in BindingDB
Kd: 200 nM  BindingMOAD
Kd: 200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.170
  • R-Value Work: 0.144
  • Space Group: P 63

Unit Cell:

Length (Å) Angle (°)
a = 54.59 α = 90.00
b = 54.59 β = 90.00
c = 83.05 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-05-15
  • Released Date: 2007-05-22
  • Deposition author(s): Barabas, O., Nagy, N., Takacs, E., Vertessy, B.G.

Revision History

  • 2008-05-01
    Type: Version format compliance
  • 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance