1N3I

Crystal Structure of Mycobacterium tuberculosis PNP with transition state analog DADMe-ImmH

Structural Biology Knowledgebase: 1N3I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 1N3I

Classification: TRANSFERASE

Total Structure Weight: 83885.77

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 MT3406 Rv3307 MTV016.06
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C 3-HYDROXY-4-HYDROXYMETHYL-1-(4-OXO-4,4A,5,7A- TETRAHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YLMETHYL)- PYRROLIDINIUM
(3R, (Synonym)
C12 H19 N4 O3
WFVGWLHAOKEIOJ-MFQSTILNSA-O
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 %)
DIH N/A in BindingDB
Kd: 1.3 nM  BindingMOAD
Ki: 1.3 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.183
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 102.84 α = 90.00
b = 102.84 β = 90.00
c = 128.76 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-28
  • Released Date: 2003-09-30
  • Deposition author(s): Lewandowicz, A., Shi, W., Evans, G.B., Tyler, P.C., Furneaux, R.H., Basso, L.A., Santos, D.S., Almo, S.C., Schramm, V.L.

Revision History

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