1E2R Oxidoreductase date May 24, 2000
title Cytochrome Cd1 Nitrite Reductase, Reduced And Cyanide Bound
authors V.Fulop
compound source
Molecule: Nitrite Reductase
Chain: A, B
Synonym: Cytochrome Cd1, Cytochrome Oxidase, Hydroxylamine Cytochrome Cd1 Nitrite Reductase;
Ec: 1.7.2.1, 1.7.99.1
 Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 266
Cellular_location: Periplasm
Other_details: Subsp. Paracoccus Pantotrophus Formally Know Thiosphaera Pantotropha
symmetry Space Group: P 1 21 1
R_factor 0.192 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.500 60.900 100.100 90.00 111.90 90.00
method X-Ray Diffractionresolution 1.59 Å
ligand CYN, DHE, GOL, HEC enzyme Oxidoreductase E.C.1.7.2.1 BRENDA
related structures by homologous chain: 1DY7, 1HJ5
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • electron transfer activity


    • Primary referenceX-ray crystallographic study of cyanide binding provides insights into the structure-function relationship for cytochrome cd1 nitrite reductase from Paracoccus pantotrophus., Jafferji A, Allen JW, Ferguson SJ, Fulop V, J Biol Chem 2000 Aug 18;275(33):25089-94. PMID:10827177
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (206 Kb) [Save to disk]
  • Biological Unit Coordinates (1e2r.pdb1.gz) 199 Kb
  • LPC: Ligand-Protein Contacts for 1E2R
  • CSU: Contacts of Structural Units for 1E2R
  • Likely Quarternary Molecular Structure file(s) for 1E2R
  • Retrieve 1E2R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1E2R from S2C, [Save to disk]
    • View 1E2R 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 1E2R
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1E2R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1e2ra2, region A:136-567 [Jmol] [rasmolscript] [script source]
        - Domain d1e2ra1, region A:36-135 [Jmol] [rasmolscript] [script source]
        - Domain d1e2rb2, region B:136-567 [Jmol] [rasmolscript] [script source]
        - Domain d1e2rb1, region B:25-135 [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: [1e2r_A] [1e2r_B] [1e2r]
  • SWISS-PROT database: [P72181]
  • Domain organization of [NIRS_PARPN] by SWISSPFAM
    • Other resources with information on 1E2R
  • Community annotation for 1E2R 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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