1YKI Oxidoreductase date Jan 18, 2005
title The Structure Of E. Coli Nitroreductase Bound With The Antib Nitrofurazone
authors P.R.Race, A.L.Lovering, R.M.Green, A.Ossor, S.A.White, P.F.Searle C.J.Wrighton, E.I.Hyde
compound source
Molecule: Oxygen-Insensitive Nad(P)H Nitroreductase
Chain: A, B, C, D
Synonym: Fmn-Dependent Nitroreductase, Dihydropteridine Red
Ec: 1.5.1.34
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Nfnb, Dpra, Nfsb, Nfsi, Ntr
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11c
symmetry Space Group: P 1 21 1
R_factor 0.144 R_Free 0.167
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.078 56.466 116.085 90.00 103.10 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand CIT, DMS, FMN, NFZ enzyme Oxidoreductase E.C.1.5.1.34 BRENDA
related structures by homologous chain: 1YLR
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme., Race PR, Lovering AL, Green RM, Ossor A, White SA, Searle PF, Wrighton CJ, Hyde EI, J Biol Chem 2005 Apr 8;280(14):13256-64. Epub 2005 Jan 31. PMID:15684426
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk]
  • Biological Unit Coordinates (1yki.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (1yki.pdb2.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 1YKI
  • CSU: Contacts of Structural Units for 1YKI
  • Likely Quarternary Molecular Structure file(s) for 1YKI
  • Structure Factors (700 Kb)
  • Retrieve 1YKI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YKI from S2C, [Save to disk]
  • Re-refined 1yki structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YKI 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 1YKI
  • 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 1YKI, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yki_C] [1yki_B] [1yki_A] [1yki] [1yki_D]
  • SWISS-PROT database: [P38489]
  • Domain organization of [NFNB_ECOLI] by SWISSPFAM
  • Other resources with information on 1YKI
  • Community annotation for 1YKI 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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