3OBK

Crystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase) from toxoplasma gondii ME49 in complex with the reaction product porphobilinogen

Structural Biology Knowledgebase: 3OBK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3OBK

Classification: LYASE

Total Structure Weight: 320090.02

Macromolecule Entities
Molecule Chains Length Organism Details
Delta-aminolevulinic acid dehydratase A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 356 Toxoplasma gondii EC#: 4.2.1.24 IUBMB
Fragment: residues 303-658
Gene Name(s):

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

A, B, C, D, E, F, G, H 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL- 3-YL]PROPANOIC ACID
2-AMINOMETHYLPYRROL-3-ACETIC ACID 4-PROPIONIC ACID; PORPHOBILINOGEN; 5- (AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROLE- 3-PROPANOIC ACID (Synonym)
C10 H14 N2 O4
QSHWIQZFGQKFMA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B, C, D, E, F, G, H 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D, E, F, G, H CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F, G, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.177
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 177.11 α = 90.00
b = 187.17 β = 90.00
c = 95.86 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-08-06
  • Released Date: 2010-09-15
  • Deposition author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History

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