1D6M Isomerase date Oct 14, 1999
title Crystal Structure Of E. Coli Dna Topoisomerase III
authors A.Mondragon, R.Digate
compound source
Molecule: Dna Topoisomerase III
Chain: A
Ec: 5.99.1.2
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hms-83
Expression_system_plasmid: Pet3
symmetry Space Group: P 61 2 2
R_factor 0.237 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
236.000 236.000 108.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand
enzyme Isomerase E.C.5.99.1.2 BRENDA
related structures by homologous chain: 1I7D
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe structure of Escherichia coli DNA topoisomerase III., Mondragon A, DiGate R, Structure Fold Des 1999 Nov 15;7(11):1373-83. PMID:10574789
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (1d6m.pdb1.gz) 89 Kb
  • CSU: Contacts of Structural Units for 1D6M
  • Likely Quarternary Molecular Structure file(s) for 1D6M
  • Retrieve 1D6M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D6M from S2C, [Save to disk]
  • View 1D6M 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 1D6M
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1D6M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d6ma_, region A [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: [1d6m_A] [1d6m]
  • SWISS-PROT database: [P14294]
  • Domain organization of [TOP3_ECOLI] by SWISSPFAM
  • Domains found in 1D6M: [TOP1Ac] [TOP1Bc] [TOPRIM ] by SMART
  • Other resources with information on 1D6M
  • Community annotation for 1D6M at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1D6M from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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