1K9S

PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN A DERIVATIVE AND PHOSPHATE

Structural Biology Knowledgebase: 1K9S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.161

Literature

Macromolecules
Sequence Display for 1K9S

Classification: TRANSFERASE

Total Structure Weight: 156591.06

Macromolecule Entities
Molecule Chains Length Organism Details
PURINE NUCLEOSIDE PHOSPHORYLASE A, B, C..., D, E, FA, B, C, D, E, F 237 Escherichia coli EC#: 2.4.2.1 IUBMB
Gene Name(s): deoD pup b4384 JW4347
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FM2
Query on FM2

A, B, C 2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,3-D]PYRIMIDIN- 3-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4- DIOL
6-METHYL-FORMYCIN A (Synonym)
C11 H16 N5 O4
UHYKIYIKTWEXSX-LFAOKBQASA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FM1
Query on FM1

D, E, F 2-HYDROXYMETHYL-5-(7-METHYLAMINO-3H-PYRAZOLO[4,3- D]PYRIMIDIN-3-YL)-TETRAHYDRO-FURAN-3,4-DIOL
N7-METHYL-FORMYCIN A (Synonym)
C11 H15 N5 O4
JRRNRCMIBCSOIH-LFAOKBQASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C, D, E, F PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FM2 N/A in BindingDB
N/A in BindingMoad
Ki: 300 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.161
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 178.78 α = 90.00
b = 178.78 β = 90.00
c = 167.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-10-30
  • Released Date: 2001-11-28
  • Deposition author(s): Koellner, G., Bzowska, A., Wielgus-Kutrowska, B., Luic, M., Steiner, T., Saenger, W., Stepinski, J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4