1UPD Electron Transport date Sep 29, 2003
title Oxidized Structure Of Cytochrome C3 From Desulfovibrio Desul Atcc 27774 At Ph 7.6
authors I.Bento, P.M.Matias, A.M.Baptista, P.N.Da Costa, W.M.A.M.Van Don L.M.Saraiva, T.R.Schneider, C.M.Soares, M.A.Carrondo
compound source
Molecule: Cytochrome C3
Chain: A
Synonym: Cytc3
 Organism_scientific: Desulfovibrio Desulfuricans
Organism_taxid: 876
Atcc: 27774
symmetry Space Group: P 61 2 2
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.680 61.680 106.120 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.40 Å
ligand HEC enzyme
related structures by homologous chain: 1UP9, 3CYR
Gene
Ontology
ChainFunctionProcessComponent
A
  • electron transfer activity


    • Primary referenceMolecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6., Bento I, Matias PM, Baptista AM, da Costa PN, van Dongen WM, Saraiva LM, Schneider TR, Soares CM, Carrondo MA, Proteins. 2004 Jan 1;54(1):135-52. PMID:14705030
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (1upd.pdb1.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 1UPD
  • CSU: Contacts of Structural Units for 1UPD
  • Likely Quarternary Molecular Structure file(s) for 1UPD
  • Structure Factors (230 Kb)
  • Retrieve 1UPD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UPD from S2C, [Save to disk]
  • Re-refined 1upd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1UPD 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 1UPD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 1UPD from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1UPD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1upda_, region A [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: [1upd] [1upd_A]
  • SWISS-PROT database: [Q9L915]
  • Domain organization of [Q9L915_DESDE] by SWISSPFAM
    • Other resources with information on 1UPD
  • Community annotation for 1UPD 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