3PHY Photoreceptor date Feb 06, 1998
title Photoactive Yellow Protein, Dark State (Unbleached), Solutio Structure, Nmr, 26 Structures
authors P.Dux, G.Rubinstenn, G.W.Vuister, R.Boelens, F.A.A.Mulder, K.Hard W.D.Hoff, A.Kroon, W.Crielaard, K.J.Hellingwerf, R.Kaptein
compound source
Molecule: Photoactive Yellow Protein
Chain: A
Synonym: Pyp
 Organism_scientific: Halorhodospira Halophila
Organism_taxid: 1053
Strain: Bn9626
methodSolution NMR
ligand HC4 enzyme
related structures by homologous chain: 1S4S
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSolution structure and backbone dynamics of the photoactive yellow protein., Dux P, Rubinstenn G, Vuister GW, Boelens R, Mulder FA, Hard K, Hoff WD, Kroon AR, Crielaard W, Hellingwerf KJ, Kaptein R, Biochemistry 1998 Sep 15;37(37):12689-99. PMID:9737845
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (836 Kb) [Save to disk]
  • Biological Unit Coordinates (3phy.pdb1.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 3PHY
  • CSU: Contacts of Structural Units for 3PHY
  • Original NMR restraints for 3PHY from PDB
  • Retrieve 3PHY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PHY from S2C, [Save to disk]
    • View 3PHY 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 3PHY
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3PHY, from MSDmotif at EBI
  • Genome occurence of 3PHY's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d3phy__, region [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: [3phy] [3phy_A]
  • SWISS-PROT database: [P16113]
  • Domain organization of [PYP_HALHA] by SWISSPFAM
  • Domain found in 3PHY: [PAS ] by SMART
    • Other resources with information on 3PHY
  • Community annotation for 3PHY at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Domain movements in 3PHY from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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