1D7E Photosynthesis date Oct 17, 1999
title Crystal Structure Of The P65 Crystal Form Of Photoactive Yel Protein
authors D.M.F.Van Aalten, W.Crielaard, K.J.Hellingwerf, L.Joshua-Tor
compound source
Molecule: Photoactive Yellow Protein
Chain: A
Synonym: Pyp
Engineered: Yes
Organism_scientific: Halorhodospira Halophila
Organism_taxid: 1053
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: M15
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phisp
symmetry Space Group: P 65
length a length b length c angle alpha angle beta angle gamma
40.561 40.561 118.089 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.39 Å
ligand HC4 enzyme
related structures by homologous chain: 1OTD, 1OTI

Primary referenceConformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility., van Aalten DM, Crielaard W, Hellingwerf KJ, Joshua-Tor L, Protein Sci 2000 Jan;9(1):64-72. PMID:10739248
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (1d7e.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 1D7E
  • CSU: Contacts of Structural Units for 1D7E
  • Likely Quarternary Molecular Structure file(s) for 1D7E
  • Retrieve 1D7E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D7E from S2C, [Save to disk]
  • View 1D7E 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 1D7E
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1D7E from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1D7E, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d7ea_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1d7e 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: [1d7e] [1d7e_A]
  • SWISS-PROT database: [P16113]
  • Domain organization of [PYP_HALHA] by SWISSPFAM
  • Domain found in 1D7E: [PAS ] by SMART
  • Other resources with information on 1D7E
  • Community annotation for 1D7E 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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