4APY Oxidoreductase date Apr 09, 2012
title Ethylene Glycol-Bound Form Of P450 Cyp125a3 From Mycobacteri Smegmatis
authors D.J.Frank, E.Garcia Fernandez, P.M.Kells, J.L.Garcia Lopez, L.M. P.R.Ortiz De Montellano
compound source
Molecule: P450 Heme-Thiolate Protein
Chain: A
Synonym: Cyp125a3
Engineered: Yes
 Organism_scientific: Mycobacterium Smegmatis Str. Mc2 155
Organism_taxid: 246196
Expression_system: Escherichia Coli Dh5[Alpha]
Expression_system_taxid: 668369
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcw
symmetry Space Group: I 41
R_factor 0.164 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.188 108.188 120.234 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CL, EDO, HEM enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA highly conserved mycobacterial cholesterol catabolic pathway., Garcia-Fernandez E, Frank DJ, Galan B, Kells PM, Podust LM, Garcia JL, Ortiz de Montellano PR, Environ Microbiol. 2013 Feb 19. doi: 10.1111/1462-2920.12108. PMID:23489718
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (4apy.pdb1.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 4APY
  • CSU: Contacts of Structural Units for 4APY
  • Structure Factors (2431 Kb)
  • Retrieve 4APY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4APY from S2C, [Save to disk]
  • Re-refined 4apy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4APY 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 4APY
  • 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 4APY, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4apy_A] [4apy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4APY
  • Community annotation for 4APY at PDBWiki (http://pdbwiki.org)

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