1L6Y

Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid

Structural Biology Knowledgebase: 1L6Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 1L6Y

Classification: LYASE

Total Structure Weight: 72300.26

Macromolecule Entities
Molecule Chains Length Organism Details
PORPHOBILINOGEN SYNTHASE A, B 323 Escherichia coli EC#: 4.2.1.24 IUBMB
Mutation: C133X
Gene Name(s): hemB ncf b0369 JW0361
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
4OX
Query on 4OX

A, B 4-OXODECANEDIOIC ACID
4-OXOSEBACIC ACID (Synonym)
C10 H16 O5
XTQIBFVBYWIHIP-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-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 %)
4OX N/A in BindingDB
N/A in BindingMoad
IC50: 220000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A, B L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.206
  • Space Group: P 4 21 2

Unit Cell:

Length (Å) Angle (°)
a = 129.00 α = 90.00
b = 129.00 β = 90.00
c = 142.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-03-14
  • Released Date: 2002-04-17
  • Deposition author(s): Jaffe, E.K., Kervinen, J., Martins, J., Stauffer, F., Neier, R., Wlodawer, A., Zdanov, A.

Revision History

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