1I80

CRYSTAL STRUCTURE OF M. TUBERCULOSIS PNP IN COMPLEX WITH IMINORIBITOL, 9-DEAZAHYPOXANTHINE AND PHOSPHATE ION

Structural Biology Knowledgebase: 1I80 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 1I80

Classification: TRANSFERASE

Total Structure Weight: 83432.42

Macromolecule Entities
Molecule Chains Length Organism Details
PURINE NUCLEOSIDE PHOSPHORYLASE A, B, C 268 Mycobacterium tuberculosis EC#: 2.4.2.1 IUBMB
Gene Name(s): punA deoD Rv3307 MTV016.06
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
9HX
Query on 9HX

A, B, C 9-DEAZAHYPOXANTHINE
C6 H5 N3 O
UWMXUDUWVFWJPX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMR
Query on IMR

A IMINORIBITOL
4-DIOL, (Synonym)
C5 H11 N O3
OQEBIHBLFRADNM-MROZADKFSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
9HX N/A in BindingDB
Kd: 390 nM  BindingMOAD
Kd: 390 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.206
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 119.98 α = 90.00
b = 135.77 β = 90.00
c = 45.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-03-12
  • Released Date: 2001-08-01
  • Deposition author(s): Shi, W., Basso, L.A., Tyler, P.C., Furneaux, R.H., Blanchard, J.S., Almo, S.C., Schramm, V.L.

Revision History

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