1B8O

PURINE NUCLEOSIDE PHOSPHORYLASE

Structural Biology Knowledgebase: 1B8O SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.184

Literature

Macromolecules
Sequence Display for 1B8O

Classification: TRANSFERASE

Total Structure Weight: 32072.86

Macromolecule Entities
Molecule Chains Length Organism Details
PURINE NUCLEOSIDE PHOSPHORYLASE A 284 Bos taurus EC#: 2.4.2.1 IUBMB
Details: COMPLEXED WITH TRANSITION-STATE ANALOGUE 1,4-DIDEOXY-1,4-IMINO-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL
Gene Name(s): PNP Gene View NP
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN- 9-YL)-D-RIBITOL
C11 H14 N4 O4
IWKXDMQDITUYRK-KUBHLMPHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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 %)
IMH IC50: 3.5 - 100 nM (88) BindingDB
Kd: 0.023 - 0.058 nM (88 - 99) BindingDB
Ki: 0.056 - 56 nM (88 - 99) BindingDB

Ki: 0.023 nM  BindingMOAD
Ki: 0.023 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.184
  • Space Group: P 21 3

Unit Cell:

Length (Å) Angle (°)
a = 92.68 α = 90.00
b = 92.68 β = 90.00
c = 92.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-02-02
  • Released Date: 1999-02-08
  • Deposition author(s): Fedorov, A.A., Kicska, G.A., Fedorov, E.V., Shi, W., Tyler, P.C., Furneaux, R.H., Schramm, V.L., Almo, S.C.

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