1PKE

Crystal Structure of E. coli purine nucleoside phosphorylase complexed with 2-fluoro-2'-deoxyadenosine and sulfate/phosphate

Structural Biology Knowledgebase: 1PKE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.173

Literature

Macromolecules
Sequence Display for 1PKE

Classification: TRANSFERASE

Total Structure Weight: 78257.91

Macromolecule Entities
Molecule Chains Length Organism Details
Purine nucleoside phosphorylase A, B, C 237 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
2FD
Query on 2FD

A, B, C 5-(6-AMINO-2-FLUORO-PURIN-9-YL)-2-HYDROXYMETHYL- TETRAHYDRO-FURAN-3-OL
2-FLUORO-2'-DEOXYADENOSINE (Synonym)
C10 H12 F N5 O3
ZWPYUXAXLRFWQC-KVQBGUIXSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.173
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 122.70 α = 90.00
b = 122.70 β = 90.00
c = 243.70 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-05
  • 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