1I8J

CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID

Structural Biology Knowledgebase: 1I8J SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 1I8J

Classification: LYASE

Total Structure Weight: 71715.54

Macromolecule Entities
Molecule Chains Length Organism Details
PORPHOBILINOGEN SYNTHASE A, B 323 Escherichia coli EC#: 4.2.1.24 IUBMB
Gene Name(s): hemB ncf b0369 JW0361
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 4,7-DIOXOSEBACIC ACID
C10 H14 O6
DUAWJQCMZICMIK-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-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 %)
DSB N/A in BindingDB
N/A in BindingMoad
IC50: 39000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.198
  • Space Group: P 4 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.74 α = 90.00
b = 128.74 β = 90.00
c = 142.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-03-14
  • Released Date: 2001-06-20
  • Deposition author(s): Kervinen, J., Jaffe, E.K., Stauffer, F., Neier, R., Wlodawer, A., Zdanov, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values