1SEZ

Crystal Structure of Protoporphyrinogen IX Oxidase

Structural Biology Knowledgebase: 1SEZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.293
  • R-Value Work: 0.227

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1SEZ

Classification: OXIDOREDUCTASE

Total Structure Weight: 114768.67

Macromolecule Entities
Molecule Chains Length Organism Details
Protoporphyrinogen oxidase, mitochondrial A, B 504 Nicotiana tabacum EC#: 1.3.3.4 IUBMB
Mutation: M69M, M130M, M186M, M242M, M302M, M312M, M376M, M377M, M456M
Gene Name(s): PPXII PPOX2

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

A, B FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OMN
Query on OMN

A, B 4-BROMO-3-(5'-CARBOXY-4'-CHLORO-2'-FLUOROPHENYL)- 1-METHYL-5-TRIFLUOROMETHYL-PYRAZOL
C12 H6 Br Cl F4 N2 O2
YNMHKERYELPEEF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TON
Query on TON

A, B 2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL
C18 H30 O3
LBCZOTMMGHGTPH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.293
  • R-Value Work: 0.227
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 119.09 α = 90.00
b = 147.25 β = 90.00
c = 127.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-02-19
  • Released Date: 2004-04-13
  • Deposition author(s): Koch, M., Breithaupt, C., Kiefersauer, R., Freigang, J., Huber, R., Messerschmidt, A.

Revision History

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