1OTD Signaling Protein date Mar 21, 2003
title Strong Hydrogen Bonds In Photoactive Yellow Protein And Thei Its Photocycle
authors S.Anderson, S.Crosson, K.Moffat
compound source
Molecule: Photoactive Yellow Protein
Chain: A, B
Synonym: Pyp
Engineered: Yes
Organism_scientific: Halorhodospira Halophila
Organism_taxid: 1053
Gene: Pyp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Sl-1
symmetry Space Group: P 1 21 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
33.983 91.102 36.756 90.00 92.67 90.00
method X-Ray Diffractionresolution 1.25 Å
ligand HC4 enzyme
related structures by homologous chain: 1D7E, 1UGU
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceShort hydrogen bonds in photoactive yellow protein., Anderson S, Crosson S, Moffat K, Acta Crystallogr D Biol Crystallogr 2004 Jun;60(Pt 6):1008-16. Epub 2004, May 21. PMID:15159559
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (1otd.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (1otd.pdb2.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 1OTD
  • CSU: Contacts of Structural Units for 1OTD
  • Likely Quarternary Molecular Structure file(s) for 1OTD
  • Structure Factors (577 Kb)
  • Retrieve 1OTD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OTD from S2C, [Save to disk]
  • Re-refined 1otd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1OTD 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 1OTD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1OTD 1OTDA 1OTDB from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1OTD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1otda_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1otdb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1otd 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: [1otd_A] [1otd] [1otd_B]
  • SWISS-PROT database: [P16113]
  • Domain organization of [PYP_HALHA] by SWISSPFAM
  • Domain found in 1OTD: [PAS ] by SMART
  • Other resources with information on 1OTD
  • Community annotation for 1OTD 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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