1I7D Isomerase Dna date Mar 08, 2001
title Noncovalent Complex Of E.Coli Dna Topoisomerase III With An 8-Base Single-Stranded Dna Oligonucleotide
authors A.Changela, R.J.Digate, A.Mondragon
compound source
Molecule: 5'-D(Cpgpcpapapcptpt)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Dna Topoisomerase III
Chain: A
Ec: 5.99.1.2
Engineered: Yes
Mutation: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Hms-83
Gene: Topb
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21
symmetry Space Group: C 1 2 1
R_factor 0.233 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
122.011 60.831 125.358 90.00 90.73 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand CL, SO4 enzyme Isomerase E.C.5.99.1.2 BRENDA
related structures by homologous chain: 1D6M
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule., Changela A, DiGate RJ, Mondragon A, Nature 2001 Jun 28;411(6841):1077-81. PMID:11429611
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (1i7d.pdb1.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 1I7D
  • CSU: Contacts of Structural Units for 1I7D
  • Likely Quarternary Molecular Structure file(s) for 1I7D
  • Retrieve 1I7D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1I7D from S2C, [Save to disk]
  • View 1I7D 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 1I7D
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1I7D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1i7da_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1i7d 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: [1i7d] [1i7d_B] [1i7d_A]
  • SWISS-PROT database: [P14294]
  • Domain organization of [TOP3_ECOLI] by SWISSPFAM
  • Domains found in 1I7D: [TOP1Ac] [TOP1Bc] [TOPRIM ] by SMART
  • Other resources with information on 1I7D
  • Community annotation for 1I7D 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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