1DUD

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE (D-UTPASE) COMPLEXED WITH THE SUBSTRATE ANALOGUE DEOXYURIDINE 5'-DIPHOSPHATE (D-UDP)

Structural Biology Knowledgebase: 1DUD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.200

Literature

Macromolecules
Sequence Display for 1DUD

Classification: HYDROLASE

Total Structure Weight: 16690.90

Macromolecule Entities
Molecule Chains Length Organism Details
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE A 152 Escherichia coli EC#: 3.6.1.23 IUBMB
Gene Name(s): dut dnaS sof b3640 JW3615
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A DEOXYURIDINE-5'-DIPHOSPHATE
C9 H14 N2 O11 P2
QHWZTVCCBMIIKE-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DUD N/A in BindingDB
Ki: 15000 nM  BindingMOAD
Ki: 15000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.200
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 86.64 α = 90.00
b = 86.64 β = 90.00
c = 62.23 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1996-04-30
  • Released Date: 1996-11-08
  • Deposition author(s): Larsson, G., Svensson, L.A., Nyman, P.O.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4