1PR5

Escherichia coli Purine Nucleoside Phosphorylase Complexed with 7-deazaadenosine and Phosphate/Sulfate

Structural Biology Knowledgebase: 1PR5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 1PR5

Classification: TRANSFERASE

Total Structure Weight: 79029.91

Macromolecule Entities
Molecule Chains Length Organism Details
Purine nucleoside phosphorylase A, B, C 239 Escherichia coli EC#: 2.4.2.1 IUBMB
Gene Name(s): deoD Z5986 ECs5343
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C '2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)- 5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL
7-DEAZAADENOSINE (Synonym)
C11 H14 N4 O4
HDZZVAMISRMYHH-KCGFPETGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TBN N/A in BindingDB
Ki: 120000 nM  BindingMOAD
Ki: 120000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.207
  • Space Group: P 61 2 2

Unit Cell:

Length (Å) Angle (°)
a = 120.80 α = 90.00
b = 120.80 β = 90.00
c = 239.90 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-19
  • Released Date: 2003-11-25
  • Deposition author(s): Bennett, E.M., Li, C., Allan, P.W., Parker, W.B., Ealick, S.E.

Revision History

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