1DNP Lyase (Carbon-Carbon) date Jul 03, 1995
title Structure Of Deoxyribodipyrimidine Photolyase
authors H.W.Park, A.Sancar, J.Deisenhofer
compound source
Molecule: Dna Photolyase
Chain: A, B
Synonym: Dna Cyclobutane Dipyrimidine Photolyase
Ec: 4.1.99.3
Other_details: Photoreactivating Enzyme
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 1
R_factor 0.172 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.600 72.200 58.500 99.10 101.50 72.00
method X-Ray Diffractionresolution 2.30 Å
ligand FAD, MHF enzyme Lyase E.C.4.1.99.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of DNA photolyase from Escherichia coli., Park HW, Kim ST, Sancar A, Deisenhofer J, Science 1995 Jun 30;268(5219):1866-72. PMID:7604260
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (164 Kb) [Save to disk]
  • Biological Unit Coordinates (1dnp.pdb1.gz) 81 Kb
  • Biological Unit Coordinates (1dnp.pdb2.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 1DNP
  • CSU: Contacts of Structural Units for 1DNP
  • Likely Quarternary Molecular Structure file(s) for 1DNP
  • Structure Factors (408 Kb)
  • Retrieve 1DNP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DNP from S2C, [Save to disk]
  • Re-refined 1dnp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1DNP 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 1DNP
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1DNP, from MSDmotif at EBI
  • Genome occurence of 1DNP's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dnpa2, region A:1-200 [Jmol] [rasmolscript] [script source]
        - Domain d1dnpa1, region A:201-469 [Jmol] [rasmolscript] [script source]
        - Domain d1dnpb2, region B:1-200 [Jmol] [rasmolscript] [script source]
        - Domain d1dnpb1, region B:201-469 [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: [1dnp] [1dnp_B] [1dnp_A]
  • SWISS-PROT database: [P00914]
  • Domain organization of [PHR_ECOLI] by SWISSPFAM
    • Other resources with information on 1DNP
  • Community annotation for 1DNP at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Domain movements in 1DNP from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science