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 Diffraction	resolution	1.40 Å
ligand	HC4	enzyme
note	2PHY supersedes 1PHY
related structures	by homologous chain: 1OTE, 1S1Z
Gene Ontology	Chain Function Process Component A
Primary reference	1.4 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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