1D7Y Oxidoreductase date Oct 21, 1999
title Crystal Structure Of Nadh-Dependent Ferredoxin Reductase, Bp
authors T.Senda, T.Yamada, N.Sakurai, M.Kubota, T.Nishizaki, E.Masai, M.Fu Y.Mitsui
compound source
Molecule: Ferredoxin Reductase
Chain: A
Engineered: Yes
 Organism_scientific: Pseudomonas Sp.
Organism_taxid: 307
Strain: Kks102
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 61 2 2
R_factor 0.183 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.200 99.200 175.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand FAD enzyme
related structures by homologous chain: 1F3P
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase., Senda T, Yamada T, Sakurai N, Kubota M, Nishizaki T, Masai E, Fukuda M, Mitsuidagger Y, J Mol Biol 2000 Dec 1;304(3):397-410. PMID:11090282
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (1d7y.pdb1.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 1D7Y
  • CSU: Contacts of Structural Units for 1D7Y
  • Likely Quarternary Molecular Structure file(s) for 1D7Y
  • Retrieve 1D7Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D7Y from S2C, [Save to disk]
    • View 1D7Y 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 1D7Y
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1D7Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d7ya2, region A:116-236 [Jmol] [rasmolscript] [script source]
        - Domain d1d7ya3, region A:309-405 [Jmol] [rasmolscript] [script source]
        - Domain d1d7ya1, region A:5-115,A:237-308 [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: [1d7y_A] [1d7y]
  • SWISS-PROT database: [Q52437]
  • Domain organization of [Q52437_PSES1] by SWISSPFAM
    • Other resources with information on 1D7Y
  • Community annotation for 1D7Y 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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