2PHY Photoreceptor date Apr 12, 1995
title Photoactive Yellow Protein, Dark State (Unbleached)
authors G.E.O.Borgstahl, E.D.Getzoff
compound source
Molecule: Photoactive Yellow Protein
Chain: A
Synonym: Pyp
Organism_scientific: Halorhodospira Halophila
Organism_taxid: 1053
Strain: Bn9626
symmetry Space Group: P 63
R_factor 0.186 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.900 66.900 40.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.40 Å
ligand HC4 enzyme
note 2PHY supersedes 1PHY
related structures by homologous chain: 1OTE, 1S1Z
Gene
Ontology
ChainFunctionProcessComponent
A


Primary reference1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore., Borgstahl GE, Williams DR, Getzoff ED, Biochemistry 1995 May 16;34(19):6278-87. PMID:7756254
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (26 Kb) [Save to disk]
  • Biological Unit Coordinates (2phy.pdb1.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 2PHY
  • CSU: Contacts of Structural Units for 2PHY
  • Likely Quarternary Molecular Structure file(s) for 2PHY
  • Retrieve 2PHY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PHY from S2C, [Save to disk]
  • View 2PHY 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 2PHY
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 2PHY from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2PHY, from MSDmotif at EBI
  • Genome occurence of 2PHY's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2phy__, region [Jmol] [rasmolscript] [script source]
  • Fold representative 2phy from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [2phy_A] [2phy]
  • SWISS-PROT database: [P16113]
  • Domain organization of [PYP_HALHA] by SWISSPFAM
  • Domain found in 2PHY: [PAS ] by SMART
  • Other resources with information on 2PHY
  • Community annotation for 2PHY at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 2PHY from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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