1Q54

STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH THE BROMOHYDRINE OF IPP

Structural Biology Knowledgebase: 1Q54 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 1Q54

Classification: ISOMERASE

Total Structure Weight: 42069.47

Macromolecule Entities
Molecule Chains Length Organism Details
ISOPENTENYL DIPHOSPHATE DELTA-ISOMERASE A, B 183 Escherichia coli EC#: 5.3.3.2 IUBMB
Mutation: C67A
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
BHI
Query on BHI

A, B 4-BROMO-3-HYDROXY-3-METHYL BUTYL DIPHOSPHATE
C5 H13 Br O8 P2
YKAYCWPQDPILSA-RXMQYKEDSA-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 %)
BHI N/A in BindingDB
Ki: 1400 nM  BindingMOAD
Ki: 1400 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.210
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.83 α = 90.00
b = 71.35 β = 90.00
c = 91.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-08-06
  • Released Date: 2003-08-26
  • Deposition author(s): Wouters, J., Oudjama, Y., Ghosh, S., Stalon, V., Droogmans, L.
  • Previous versions: 1N2U

Revision History

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