3NKS Oxidoreductase Oxidoreductase Inhibitor date Jun 21, 2010
title Structure Of Human Protoporphyrinogen Ix Oxidase
authors Y.Shen
compound source
Molecule: Protoporphyrinogen Oxidase
Chain: A
Synonym: Protoporphyrinogen Ix Oxidase, Ppo
Ec: 1.3.3.4
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ppox
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
symmetry Space Group: H 3 2
R_factor 0.206 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
136.702 136.702 158.877 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACJ, FAD, GOL BindingDB enzyme Oxidoreductase E.C.1.3.3.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural insight into human variegate porphyria disease., Qin X, Tan Y, Wang L, Wang Z, Wang B, Wen X, Yang G, Xi Z, Shen Y, FASEB J. 2011 Feb;25(2):653-64. Epub 2010 Nov 3. PMID:21048046
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (3nks.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (3nks.pdb2.gz) 152 Kb
  • LPC: Ligand-Protein Contacts for 3NKS
  • CSU: Contacts of Structural Units for 3NKS
  • Structure Factors (518 Kb)
  • Retrieve 3NKS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NKS from S2C, [Save to disk]
  • Re-refined 3nks structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3NKS in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3NKS
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3NKS, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nks] [3nks_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3NKS
  • Community annotation for 3NKS at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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