4ZAD Lyase date Apr 13, 2015
title Structure Of C. Dubliensis Fdc1 With The Prenylated-Flavin C The Iminium Form.
authors S.S.Bailey, D.Leys
compound source
Molecule: Fdc1
Chain: A, B
Engineered: Yes
Organism_scientific: Candida Dubliniensis
Organism_common: Yeast
Organism_taxid: 42374
Gene: Cd36_64160
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.205 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.970 64.550 96.050 90.00 91.07 90.00
method X-Ray Diffractionresolution 2.46 Å
ligand 4LU, K, MN enzyme
Gene CD36
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceNew cofactor supports alpha,beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition., Payne KA, White MD, Fisher K, Khara B, Bailey SS, Parker D, Rattray NJ, Trivedi DK, Goodacre R, Beveridge R, Barran P, Rigby SE, Scrutton NS, Hay S, Leys D, Nature. 2015 Jun 25;522(7557):497-501. doi: 10.1038/nature14560. Epub 2015 Jun, 17. PMID:26083754
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (172 Kb) [Save to disk]
  • Biological Unit Coordinates (4zad.pdb1.gz) 166 Kb
  • LPC: Ligand-Protein Contacts for 4ZAD
  • CSU: Contacts of Structural Units for 4ZAD
  • Structure Factors (758 Kb)
  • Retrieve 4ZAD in mmCIF format [Save to disk]
  • Re-refined 4zad structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ZAD 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 4ZAD
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4ZAD, from MSDmotif at EBI
  • Fold representative 4zad from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4zad] [4zad_A] [4zad_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4ZAD
  • Community annotation for 4ZAD at PDBWiki (http://pdbwiki.org)

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