1NFS

STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPP

Structural Biology Knowledgebase: 1NFS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 1NFS

Classification: ISOMERASE

Total Structure Weight: 41945.78

Macromolecule Entities
Molecule Chains Length Organism Details
ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE A, B 183 Escherichia coli EC#: 5.3.3.2 IUBMB
Gene Name(s): idi ygfV b2889 JW2857
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE
C4 H13 N O7 P2
QGKJQRINUQGSJM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DED N/A in BindingDB
Kd: 0.12 nM  BindingMOAD
Kd: <0.12 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.210
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 68.98 α = 90.00
b = 71.49 β = 90.00
c = 91.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-16
  • Released Date: 2003-06-24
  • Deposition author(s): Wouters, J.

Revision History

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