4AOO

B. subtilis dUTPase YncF in complex with dU PPi and Mg in H32

Structural Biology Knowledgebase: 4AOO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.163

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AOO

Classification: HYDROLASE

Total Structure Weight: 67536.38

Macromolecule Entities
Molecule Chains Length Organism Details
PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF A, B, C, D 144 Bacillus subtilis EC#: 3.6.1.23 IUBMB
Gene Name(s): yncF BSU17660
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DUR
Query on DUR

A, B, C, D 2'-DEOXYURIDINE
C9 H12 N2 O5
MXHRCPNRJAMMIM-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
POP
Query on POP

A, B, C, D PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.163
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 146.63 α = 90.00
b = 146.63 β = 90.00
c = 144.80 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-29
  • Released Date: 2013-04-17
  • Deposition author(s): Garcia-Nafria, J., Timm, J., Harrison, C., Turkenburg, J.P., Wilson, K.S.

Revision History

  • 2013-08-07
    Type: Citation | Details: JRNL
  • 2013-07-31
    Type: Entry authorship | Details: AUTHOR
  • 2013-07-31
    Type: Citation | Details: JRNL