1CYY Isomerase date Aug 31, 1999
title Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna Topo I. Hexagonal Form
authors H.Feinberg, C.Lima, A.Mondragon
compound source
Molecule: Dna Topoisomerase I
Chain: A, B
Fragment: 30 Kda Fragment Comprising Domains II And III
Ec: 5.99.1.2
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5 Alpha
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t
symmetry Space Group: P 61 2 2
R_factor 0.229 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.850 113.850 233.870 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.15 Å
ligand ZN enzyme Isomerase E.C.5.99.1.2 BRENDA
related structures by homologous chain: 1CY2, 1MW8
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceConformational changes in E. coli DNA topoisomerase I., Feinberg H, Lima CD, Mondragon A, Nat Struct Biol 1999 Oct;6(10):918-22. PMID:10504724
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (1cyy.pdb1.gz) 85 Kb
  • Biological Unit Coordinates (1cyy.pdb2.gz) 170 Kb
  • Biological Unit Coordinates (1cyy.pdb3.gz) 86 Kb
  • LPC: Ligand-Protein Contacts for 1CYY
  • CSU: Contacts of Structural Units for 1CYY
  • Likely Quarternary Molecular Structure file(s) for 1CYY
  • Retrieve 1CYY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1CYY from S2C, [Save to disk]
  • View 1CYY 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 1CYY
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1CYY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1cyya_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1cyyb_, region B [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: [1cyy_B] [1cyy] [1cyy_A]
  • SWISS-PROT database: [P06612]
  • Domain organization of [TOP1_ECOLI] by SWISSPFAM
  • Domain found in 1CYY: [TOP1Ac ] by SMART
  • Other resources with information on 1CYY
  • Community annotation for 1CYY 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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