1VYD Electron Transport date Apr 27, 2004
title Crystal Structure Of Cytochrome C2 Mutant G95e
authors C.Dumortier, J.Fitch, F.Van Petegem, W.Vermeulen, T.E.Meyer, J.J. Beeumen, M.A.Cusanovich
compound source
Molecule: Cytochrome C2
Chain: A, B
Engineered: Yes
Mutation: Yes
 Organism_scientific: Rhodobacter Capsulatus
Organism_taxid: 1061
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: H 3 2
R_factor 0.198 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.230 100.230 162.150 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand HEM enzyme
related structures by homologous chain: 1C2R
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • electron transfer activity


    • Primary referenceProtein dynamics in the region of the sixth ligand methionine revealed by studies of imidazole binding to Rhodobacter capsulatus cytochrome c2 hinge mutants., Dumortier C, Fitch J, Van Petegem F, Vermeulen W, Meyer TE, Van Beeumen JJ, Cusanovich MA, Biochemistry 2004 Jun 22;43(24):7717-24. PMID:15196014
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (1vyd.pdb1.gz) 20 Kb
  • Biological Unit Coordinates (1vyd.pdb2.gz) 20 Kb
  • LPC: Ligand-Protein Contacts for 1VYD
  • CSU: Contacts of Structural Units for 1VYD
  • Likely Quarternary Molecular Structure file(s) for 1VYD
  • Structure Factors (185 Kb)
  • Retrieve 1VYD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VYD from S2C, [Save to disk]
  • Re-refined 1vyd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VYD 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 1VYD
  • 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 1VYD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vyda_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vydb_, region B [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: [1vyd_B] [1vyd_A] [1vyd]
  • SWISS-PROT database: [P00094]
  • Domain organization of [CYC2_RHOCA] by SWISSPFAM
    • Other resources with information on 1VYD
  • Community annotation for 1VYD 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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