1DY7 Oxidoreductase date Jan 28, 2000
title Cytochrome Cd1 Nitrite Reductase, Co Complex
authors T.Sjogren, M.Svensson-Ek, J.Hajdu, P.Brzezinski
compound source
Molecule: Nitrite Reductase
Chain: A, B
Synonym: Cytochrome Cd1, Cytochrome Oxidase, Hydroxylamine
Organism_scientific: Paracoccus Pantotrophus
Organism_taxid: 82367
Cellular_location: Periplasm
Other_details: Organism Formerly Known As Thiosphaera Panto
symmetry Space Group: P 1 21 1
R_factor 0.178 R_Free 0.199
length a length b length c angle alpha angle beta angle gamma
106.940 61.040 100.390 90.00 111.77 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand CMO, DHE, GOL, HEC, SO4 enzyme Oxidoreductase E.C. BRENDA
related structures by homologous chain: 1E2R, 1HJ3
A, B
  • electron transfer activity

  • Primary referenceProton-coupled structural changes upon binding of carbon monoxide to cytochrome cd1: a combined flash photolysis and X-ray crystallography study., Sjogren T, Svensson-Ek M, Hajdu J, Brzezinski P, Biochemistry 2000 Sep 12;39(36):10967-74. PMID:10998233
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (176 Kb) [Save to disk]
  • Biological Unit Coordinates (1dy7.pdb1.gz) 169 Kb
  • LPC: Ligand-Protein Contacts for 1DY7
  • CSU: Contacts of Structural Units for 1DY7
  • Likely Quarternary Molecular Structure file(s) for 1DY7
  • Structure Factors (1052 Kb)
  • Retrieve 1DY7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DY7 from S2C, [Save to disk]
  • Re-refined 1dy7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DY7 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 1DY7
  • 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 1DY7, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dy7a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dy7b2, region B:136-567 [Jmol] [rasmolscript] [script source]
        - Domain d1dy7b1, region B:32-135 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dy7] [1dy7_A] [1dy7_B]
  • SWISS-PROT database: [P72181]
  • Domain organization of [NIRS_PARPN] by SWISSPFAM
  • Other resources with information on 1DY7
  • Community annotation for 1DY7 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science